scholarly journals A comprehensive approach towards the systematics of Cervidae

2019 ◽  
Author(s):  
Nicola S Heckeberg ◽  
Gert Wörheide
Keyword(s):  
Evolutionary History ◽  
Comparative Anatomy ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Comparative Morphology ◽  
Molecular Data ◽  
Optimality Criteria ◽  
Taxon Sampling ◽  
Phylogenetic Reconstructions ◽  
Systematic Relationships

Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub)classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervid species. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervid species. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most of the Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses of this work provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.

scholarly journals A comprehensive approach towards the systematics of Cervidae

2019 ◽  
Author(s):  
Nicola S Heckeberg ◽  
Gert Wörheide
Keyword(s):  
Evolutionary History ◽  
Comparative Anatomy ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Comparative Morphology ◽  
Molecular Data ◽  
Optimality Criteria ◽  
Taxon Sampling ◽  
Phylogenetic Reconstructions ◽  
Systematic Relationships

Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub)classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervid species. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervid species. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most of the Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses of this work provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.

scholarly journals The systematics of the Cervidae: a total evidence approach

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8114 ◽  
Author(s):  
Nicola S. Heckeberg
Keyword(s):  
Evolutionary History ◽  
Comparative Anatomy ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Molecular Data ◽  
Optimality Criteria ◽  
Total Evidence ◽  
Taxon Sampling ◽  
Phylogenetic Reconstructions ◽  
Systematic Relationships

Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.

scholarly journals Systematic relationships of five newly sequenced cervid species

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2307 ◽  
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.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

Systematics of Berberis sect. Wallichianae (Berberidaceae) of Taiwan and Luzon with description of three new species, B. schaaliae, B. ravenii, and B. pengii

Phytotaxa ◽  
2014 ◽  
Vol 184 (2) ◽  
pp. 61 ◽  
Author(s):  
Chih-Chieh Yu ◽  
Kuo-Fang Chung
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Close Relative ◽  
Multivariate Statistical Analyses ◽  
Multivariate Statistical ◽  
Taxonomic History ◽  
Three New Species ◽  
Independent Evolutionary History

Berberis sect. Wallichianae are species of evergreen shrubs that in Taiwan are found in subalpine and montane-temperate areas and which have a notoriously controversial taxonomic history. Based on multivariate statistical analyses of morphometric data and an explicitly stated species criterion, the taxonomy of the group in Taiwan and its close relative in Luzon (B. barandana) is revised and their endemicity is evaluated by molecular data. In addition to the six species recognized in the Flora of Taiwan, 2nd ed. (i.e., B. aristatoserrulata, B. brevisepala, B. chingshuiensis, B. kawakamii, B. mingetsensis, and B. tarokoensis), B. hayatana (synonymized under B. mingetsensis) and B. nantoensis (synonymized under B. brevisepala) are reinstated, and three new species (B. pengii, B. ravenii, and B. schaaliae) are described and illustrated. Phylogenetic analyses using three chloroplast DNA sequence regions (rbcL, ycf6-psbM, and psbA-trnH) place all Taiwanese species and B. barandana in a strongly supported clade derived from within the continental Asian species of sect. Wallichianae, indicating their independent evolutionary history and supporting their endemic status.

scholarly journals Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

2006 ◽  
Vol 2 (3) ◽  
pp. 451-454 ◽  
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 .

scholarly journals Morpho-phylogenetic evidence reveals new species in Rhytismataceae (Rhytismatales, Leotiomycetes, Ascomycota) from Guizhou Province, China

MycoKeys ◽  
2020 ◽  
Vol 76 ◽  
pp. 81-106
Author(s):  
Jin-Feng Zhang ◽  
Jian-Kui Liu ◽  
Kevin D. Hyde ◽  
Anusha H. Ekanayaka ◽  
Zuo-Yi Liu
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Comparative Morphology ◽  
Morphological Characters ◽  
Molecular Data ◽  
Guizhou Province ◽  
Molecular Analyses ◽  
Phylogenetic Affinities ◽  
Karst Terrains

Karst formations represent a unique eco-environment. Research in the microfungi inhabiting this area is limited. During an ongoing survey of ascomycetous microfungi from karst terrains in Guizhou Province, China, we discovered four new species, which are introduced here as Hypoderma paralinderae, Terriera karsti, T. meitanensis and T. sigmoideospora placed in Rhytismataceae, based on phylogenetic analyses and morphological characters. Molecular analyses, based on concatenated LSU-ITS-mtSSU sequence data, were used to infer phylogenetic affinities. Detail descriptions and comprehensive illustrations of these new taxa are provided and relationships with the allied species are discussed, based on comparative morphology and molecular data.

The taxonomic status of Cryptobatrachus frogs (Anura: Hemiphractidae) from the Serranía del Perijá

Zootaxa ◽  
2021 ◽  
Vol 5068 (2) ◽  
pp. 247-262
Author(s):  
FABIO LEONARDO MEZA-JOYA ◽  
ELIANA RAMOS ◽  
FERNANDO J. M. ROJAS-RUNJAIC ◽  
ANDRÉS OVALLE-PACHECO
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Morphological Traits ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Molecular Data ◽  
The Other ◽  
Taxon Sampling ◽  
Morphological Similarity ◽  
Morphological And Molecular Data

The Neotropical frog genus Cryptobatrachus includes six currently recognized species distributed throughout the northern Andes in Colombia and Venezuela. Cryptobatrachus conditus, C. pedroruizi, and C. remotus were described from the Colombian and Venezuelan slopes of the Serranía del Perijá. Due to the great morphological similarity among these species, we re-assess their taxonomic status based on morphological and molecular data from types, topotypes, and specimens from localities referred to in the original descriptions of these species. Morphometric comparisons showed that all these species are virtually indistinguishable, although some subtle qualitative differences in morphological traits distinguish C. conditus from the other species. Phylogenetic analyses of DNA sequences found that C. remotus and C. pedroruizi are not reciprocally monophyletic and exhibit low genetic divergence (< 1 %). Therefore, C. remotus should be considered a junior synonym of C. pedroruizi. This work stresses the importance of comprehensive taxon sampling in poorly explored areas, especially between neighbouring countries.  

scholarly journals Cytogenetic and comparative morphology of two allopatric populations of Astyanax altiparanae Garutti & Britski, 2000 (Teleostei: Characidae) from upper rio Paraná basin

2007 ◽  
Vol 5 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Manoela de S. Domingues ◽  
Marcelo R. Vicari ◽  
Vinícius Abilhoa ◽  
João P. Wamser ◽  
Marta M. Cestari ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Comparative Morphology ◽  
Molecular Data ◽  
Canonical Variables ◽  
Paraná Basin ◽  
Karyotype Formula ◽  
Morphological And Molecular Data ◽  
Parana Basin ◽  
Two Populations ◽  
South Brazil

The recently described fish species, Astyanax altiparanae (tetra) is common in the upper rio Paraná basin, and has been reported in the Iguaçu basin. However, its natural origin in the rio Iguaçu is questionable. In the present work, karyotypical and morphological features of two populations of Astyanax altiparanae from the upper rio Tibagi and upper rio Iguaçu were compared. Both populations showed 2n=50 chromosomes and differences in their karyotype formula, NOR-bearing chromosomes and location of heterochromatin. Morphometric data from both populations were analyzed through free-size canonical variables. Cytogenetic and morphological results were mostly coincident showing exclusive markers that reflect their degree of populational isolation. In addition to other geographic, morphological and molecular data for A. altiparanae populations from the lower rio Iguaçu and rio Paraná tributaries upstream from the Itaipu Dam (South Brazil), the present results indicate that the two populations analyzed in this study belong to different stocks. The presence of this species along the rio Iguaçu basin would be a consequence of a complex and poorly understood evolutionary history.

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

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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