Linking morphological and molecular sources to disentangle the case of Xylodon australis

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

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Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

Communications Biology ◽

10.1038/s42003-021-02017-0 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

E. Hekkala ◽

J. Gatesy ◽

A. Narechania ◽

R. Meredith ◽

M. Russello ◽

...

Keyword(s):

Ancient Dna ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Sister Group ◽

Molecular Data ◽

Sister Group Relationship ◽

Molecular Fossil ◽

Close Relationship ◽

History Of ◽

Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

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Molecular and Biological Characterisation of Turnip mosaic virus Isolates Infecting Poppy (Papaver somniferum and P. rhoeas) in Slovakia

Viruses ◽

10.3390/v10080430 ◽

2018 ◽

Vol 10 (8) ◽

pp. 430 ◽

Cited By ~ 2

Author(s):

Miroslav Glasa ◽

Katarína Šoltys ◽

Lukáš Predajňa ◽

Nina Sihelská ◽

Slavomíra Nováková ◽

...

Keyword(s):

Mosaic Virus ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Turnip Mosaic Virus ◽

Biological Assays ◽

Genetic Complexity ◽

The World ◽

History Of ◽

Virus Isolates

In recent years, the accumulated molecular data of Turnip mosaic virus (TuMV) isolates from various hosts originating from different parts of the world considerably helped to understand the genetic complexity and evolutionary history of the virus. In this work, four complete TuMV genomes (HC9, PK1, MS04, MS15) were characterised from naturally infected cultivated and wild-growing Papaver spp., hosts from which only very scarce data were available previously. Phylogenetic analyses showed the affiliation of Slovak Papaver isolates to the world-B and basal-B groups. The PK1 isolate showed a novel intra-lineage recombination pattern, further confirming the important role of recombination in the shaping of TuMV genetic diversity. Biological assays indicated that the intensity of symptoms in experimentally inoculated oilseed poppy are correlated to TuMV accumulation level in leaves. This is the first report of TuMV in poppy plants in Slovakia.

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A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

Australian Journal of Zoology ◽

10.1071/zo07007 ◽

2007 ◽

Vol 55 (2) ◽

pp. 73 ◽

Cited By ~ 33

Author(s):

Amy Driskell ◽

Les Christidis ◽

B. J. Gill ◽

Walter E. Boles ◽

F. Keith Barker ◽

...

Keyword(s):

New Zealand ◽

Evolutionary History ◽

Divergence Time ◽

Biodiversity Hotspot ◽

Passerine Birds ◽

New Family ◽

Close Relationship ◽

History Of ◽

Anthornis Melanura ◽

Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

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Cryptic species complexes in manipulative echinostomatid trematodes: when two become six

Parasitology ◽

10.1017/s0031182008005374 ◽

2008 ◽

Vol 136 (2) ◽

pp. 241-252 ◽

Cited By ~ 37

Author(s):

T. L. F. LEUNG ◽

D. B. KEENEY ◽

R. POULIN

Keyword(s):

Cryptic Species ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Single Species ◽

Distinct Species ◽

Molecular Data ◽

Spatial Segregation ◽

Small Scale ◽

Intermediate Hosts ◽

Species Complexes

SUMMARYRecent studies have shown that some digenean trematodes previously identified as single species due to the lack of distinguishing morphological characteristics actually consist of a number of genetically distinct cryptic species. We obtained mitochondrial 16S and nuclear ITS1 sequences for the redial stages of Acanthoparyphium sp. and Curtuteria australis collected from snails and whelks at various locations around Otago Peninsula, New Zealand. These two echinostomes are well-known host manipulators whose impact extends to the entire intertidal community. Using phylogenetic analyses, we found that Acanthoparyphium sp. is actually composed of at least 4 genetically distinct species, and that a cryptic species of Curtuteria occurs in addition to C. australis. Molecular data obtained for metacercariae dissected from cockle second intermediate hosts matched sequences obtained for Acanthoparyphium sp. A and C. australis rediae, respectively, but no other species. The various cryptic species of both Acanthoparyphium and Curtuteria also showed an extremely localized pattern of distribution: some species were either absent or very rare in Otago Harbour, but reached far higher prevalence in nearby sheltered inlets. This small-scale spatial segregation is unexpected as shorebird definitive hosts can disperse trematode eggs across wide geographical areas, which should result in a homogeneous mixing of the species on small geographical scales. Possible explanations for this spatial segregation of the species include sampling artefacts, local adaptation by first intermediate hosts, environmental conditions, and site fidelity of the definitive hosts.

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New aristonectine elasmosaurid plesiosaur specimens from the Early Maastrichtian of Angola and comments on paedomorphism in plesiosaurs

Netherlands Journal of Geosciences – Geologie en Mijnbouw ◽

10.1017/njg.2014.43 ◽

2015 ◽

Vol 94 (1) ◽

pp. 93-108 ◽

Cited By ~ 22

Author(s):

R. Araújo ◽

M.J. Polcyn ◽

J. Lindgren ◽

L.L. Jacobs ◽

A.S. Schulp ◽

...

Keyword(s):

New Zealand ◽

Histological Analysis ◽

Phylogenetic Analyses ◽

External Morphology ◽

Sister Taxon ◽

Close Relationship

AbstractNew elasmosaurid plesiosaur specimens are described from the Early Maastrichtian of Angola. Phylogenetic analyses reconstruct the Angolan taxon as an aristonectine elasmosaurid and the sister taxon of an unnamed form of similar age from New Zealand. Comparisons also indicate a close relationship with an unnamed form previously described from Patagonia. All of these specimens exhibit an ostensibly osteologically immature external morphology, but histological analysis of the Angolan material suggests an adult with paedomorphic traits. By extension, the similarity of the Angolan, New Zealand and Patagonian material indicates that these specimens represent a widespread paedomorphic yet unnamed taxon.

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Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz031 ◽

2019 ◽

Vol 187 (2) ◽

pp. 378-412 ◽

Cited By ~ 3

Author(s):

Fabiana Criste Massariol ◽

Daniela Maeda Takiya ◽

Frederico Falcão Salles

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Single Species ◽

Molecular Data ◽

Neotropical Region ◽

Fossil Species ◽

Divergence Time Estimation ◽

The Family ◽

Family Based

AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.

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A new species of Physaloptera (Nematoda: Spirurida) from Proechimys gardneri (Rodentia: Echimyidae) from the Amazon rainforest and molecular phylogenetic analyses of the genus

Journal of Helminthology ◽

10.1017/s0022149x19000610 ◽

2019 ◽

Vol 94 ◽

Cited By ~ 1

Author(s):

A. Maldonado ◽

R.O. Simões ◽

J. São Luiz ◽

S.F. Costa-Neto ◽

R.V. Vilela

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Amazon Rainforest ◽

Ancestral State ◽

Intermediate Hosts ◽

The Status ◽

Molecular Phylogenetic ◽

History Of ◽

A New Species

Abstract Nematodes of the genus Physaloptera are globally distributed and more than 100 species are known. Their life cycle involves insects, including beetles, cockroaches and crickets, as intermediate hosts. This study describes a new species of Physaloptera and reports molecular phylogenetic analyses to determine its relationships within the family Physalopteridae. Physaloptera amazonica n. sp. is described from the stomach of the caviomorph rodent Proechimys gardneri collected in the Amazon rainforest in the state of Acre, Brazil. The species is characterized by the male having the first and second pair of sessile papillae asymmetrically placed, lacking a median papilla-like protuberance between the third pairs of sessile papillae, differentiated by size and shape of the spicules, while females have four uterine branches. For both nuclear 18S rRNA and MT-CO1 gene-based phylogenies, we recovered Turgida sequences forming a clade nested within Physaloptera, thus making Physaloptera paraphyletic to the exclusion of Turgida, suggesting that the latter may have evolved from the former monodelphic ancestral state to a derived polydelphic state, or that some species of Physaloptera may belong to different genera. Relationships between most taxa within Physaloptera were poorly resolved in our phylogenies, producing multifurcations or a star phylogeny. The star-like pattern may be attributed to evolutionary processes where past simultaneous species diversification events took place. Physaloptera amazonica n. sp. formed an independent lineage, separately from the other species of Physaloptera, thus supporting the status of a new species. However, all molecular data suggested a closer relationship with other Neotropical species. In conclusion, we added a new species to this already largely diverse genus Physaloptera, bringing new insights to its phylogenetic relationships. Further analyses, adding more species and markers, should provide a better understanding of the evolutionary history of physalopterids.

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Phylogenetic studies of eucalypts: fossils, morphology and genomes

Proceedings of the Royal Society of Victoria ◽

10.1071/rs16002 ◽

2016 ◽

Vol 128 (1) ◽

pp. 12 ◽

Cited By ~ 12

Author(s):

Michael J. Bayly

Keyword(s):

Dna Sequencing ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Phylogenetic Studies ◽

Recent Advances ◽

History Of ◽

Morphological And Molecular Data ◽

Economic Use ◽

Insight Into

The eucalypt group includes seven genera: Eucalyptus, Corymbia, Angophora, Eucalyptopsis, Stockwellia, Allosyncarpia and Arillastrum. Knowledge of eucalypt phylogeny underpins classification of the group, and facilitates understanding of their ecology, conservation and economic use, as well as providing insight into the history of Australia’s flora. Studies of fossils and phylogenetic analyses of morphological and molecular data have made substantial contributions to understanding of eucalypt relationships and biogeography, but relationships among some genera are still uncertain, and there is controversy about generic circumscription of the bloodwood eucalypts (genus Corymbia). Relationships at lower taxonomic levels, e.g. among sections and series of Eucalyptus, are also not well resolved. Recent advances in DNA sequencing methods offer the ability to obtain large genomic datasets that will enable improved understanding of eucalypt evolution.

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Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

Biology Letters ◽

10.1098/rsbl.2006.0467 ◽

2006 ◽

Vol 2 (3) ◽

pp. 451-454 ◽

Cited By ~ 23

Author(s):

Nikos Poulakakis ◽

Aris Parmakelis ◽

Petros Lymberakis ◽

Moysis Mylonas ◽

Eleftherios Zouros ◽

...

Keyword(s):

Dna Sequence ◽

Ancient Dna ◽

Evolutionary History ◽

Eastern Mediterranean ◽

Multiple Displacement Amplification ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Mediterranean Islands ◽

Amplification Method ◽

History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

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Systematic relationships of five newly sequenced cervid species

PeerJ ◽

10.7717/peerj.2307 ◽

2016 ◽

Vol 4 ◽

pp. e2307 ◽

Cited By ~ 23

Author(s):

Nicola S. Heckeberg ◽

Dirk Erpenbeck ◽

Gert Wörheide ◽

Gertrud E. Rössner

Keyword(s):

Comparative Anatomy ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Data Set ◽

Systematic Uncertainties ◽

Mitochondrial Cytochrome B ◽

In The Wild ◽

History Of ◽

Systematic Relationships ◽

Partial Consensus

Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences forMazama bricenii,Mazama chunyi,Muntiacus atherodes,Pudu mephistophiles, andRusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties withinMuntiacuspersist and resolving phylogenetic relationships withinPuduandMazamaremain challenging.

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