Supplemental Material for 'Total evidence phylogenetic analysis supports new morphological synapomorphies for Bovidae (Mammalia, Artiodactyla). (American Museum novitates, no. 3970)'

2021 ◽  
Author(s):  
Zachary T. Calamari
Keyword(s):  
Phylogenetic Analysis ◽  
Total Evidence ◽  
American Museum

Paleontological data and molecular phylogenetic analysis

Paleobiology ◽  
1994 ◽  
Vol 20 (3) ◽  
pp. 259-273 ◽  
Author(s):  
Andrew B. Smith ◽  
D. T. J. Littlewood
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Sequence Data ◽  
Molecular Data ◽  
Total Evidence ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Sequence Data ◽  
Geological Past ◽  
Molecular Phylogenetic ◽  
Rates Of Molecular Evolution

Molecular data are becoming an indispensable tool for the reconstruction of phylogenies. Fossil molecular data remain scarce, but have the potential to resolve patterns of deep branching and provide empirical tests of tree reconstruction techniques. A total evidence approach, combining and comparing complementary morphological, molecular and stratigraphical data from both recent and fossil taxa, is advocated as the most promising way forward because there are several well-established problems that can afflict the analysis of molecular sequence data sometimes resulting in spurious tree topologies. The integration of evidence allows us to: (1) choose suitable taxa for molecular phylogenetic analysis for the question at hand; (2) discriminate between conflicting hypotheses of taxonomic relationship and phylogeny; (3) evaluate procedures and assumptions underlying methods of building trees; and (4) estimate rates of molecular evolution in the geological past. Paleontology offers a set of independent data for comparison and corroboration of analyses and provides the only direct means of calibrating molecular trees, thus giving insight into rates of molecular evolution in the geological past.

Allozyme Evidence for the Phylogeny of Giant New Caledonian Geckos (Squamata: Diplodactylidae: Rhacodactylus), with Comments on the Status of R. leachianus henkeli

1997 ◽  
Vol 45 (3) ◽  
pp. 317 ◽  
Author(s):  
D. A. Good ◽  
A. M. Bauer ◽  
R. A. Sadlier
Keyword(s):  
Phylogenetic Analysis ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Branching Pattern ◽  
Phenetic Analysis ◽  
Allozyme Data ◽  
The Status ◽  
Distance Data ◽  
Nei's Genetic Distance

The phylogenetic analysis of allozyme characters within the New Caledonian giant geckos, genus Rhacodactylus, yields a pattern of relationships that is largely congruent with that derived from morphological data. A ‘total evidence’ approach, incorporating 13 allozyme and 29 morphological characters, yields a single most-parsimonious tree with the pattern: R. auriculatus ((R. leachainus (R. ciliatus, R. chahoua)) (R. sarasinorum, R. trachyrhynchus)). A phenetic analysis based on Nei’s genetic distance data results in a similar branching pattern. The genus Pseudothecadactylus is tentatively regarded as valid because allozyme data conflict strongly with morphological data that suggest that these geckos evolved from within Rhacodactylus. Allozymes and available morphological data do not support the recognition of the recently described subspecies R. leachianus henkeli.

scholarly journals Himalayan fossils of the oldest known pantherine establish ancient origin of big cats

2014 ◽  
Vol 281 (1774) ◽  
pp. 20132686 ◽  
Author(s):  
Z. Jack Tseng ◽  
Xiaoming Wang ◽  
Graham J. Slater ◽  
Gary T. Takeuchi ◽  
Qiang Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Current Knowledge ◽  
Close Association ◽  
Total Evidence ◽  
Snow Leopard ◽  
Apex Predators ◽  
Region Of Origin ◽  
Asian Origin ◽  
Plateau Uplift ◽  
Tibetan Plateau Uplift

Pantherine felids (‘big cats’) include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene–Early Pliocene, replacing African records as the oldest pantherine. A ‘total evidence’ phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.

Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA

2000 ◽  
Vol 13 (5) ◽  
pp. 745 ◽  
Author(s):  
Daniel J. Murphy ◽  
Frank Udovicic ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Small Sample Size ◽  
Intergenic Spacer ◽  
Small Sample ◽  
Total Evidence ◽  
Trnl Intron ◽  
Intergenic Spacers ◽  
Sequence Variations ◽  
Jackknife Support

Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

scholarly journals Comparative Osteology, Phylogeny and Classification of the Eastern South American Catfish Genus Trichomycterus (Siluriformes: Trichomycteridae)

Taxonomy ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 160-191
Author(s):  
Wilson J. E. M. Costa
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Total Evidence ◽  
Valid Species ◽  
Character State ◽  
Data Set ◽  
Long Time ◽  
Osteological Characters

Trichomycterus has been considered for a long time to be the most problematic genus of the diverse neotropical subfamily Trichomycterinae. Recently, Trichomycterus was restricted to a clade from eastern South America supported by molecular data, but no unique morphological character state was found to distinguish it, making it difficult to allocate new species based on morphology alone. The objectives of this study were to conduct an osteological comparative analysis comprising a large sample of valid species of Trichomycterus, to conduct a total evidence phylogenetic analysis, combining osteological characters and a multigene database, and to propose an intrageneric classification based on the results of the phylogenetic analysis. Fifty-two osteological characters were combined with a multigene molecular data set of 2974 bp for 44 species of Trichomycterus, and 21 outgroups generated a well-supported phylogenetic tree, making it possible to delimit and diagnose intrageneric lineages, of which six subgenera are recognized. The high morphological diversity of osteological structures herein first reported for Trichomycterus from eastern South America is possibly related to some ecological specializations. This study shows that osteological characters combined with molecular data may be useful to consistently delimit and distinguish between trichomycterines, shedding light on the still persistent problems in trichomycterine systematics.

Phylogenetic Analysis of the New World Family Heterothripidae (Thysanoptera, Terebrantia) based on Morphological and Molecular Evidence

2019 ◽  
Vol 50 (5) ◽  
pp. 702-716 ◽  
Author(s):  
Veronica Pereyra ◽  
Adriano Cavalleri ◽  
Claudia Szumik ◽  
Christiane Weirauch
Keyword(s):  
Phylogenetic Analysis ◽  
New World ◽  
Sister Group ◽  
Molecular Data ◽  
Species Level ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Large Genus ◽  
Morphological And Molecular Data

The New World family Heterothripidae (~90 spp., four genera) comprises flower-feeding and ectoparasitic thrips. The monophyly of the group has remained untested and species-level relationships were unknown. Morphological (123 characters) and molecular (28S rDNA D2 and D3-D5, H3, and partial COI) data were compiled to reconstruct phylogenetic relationships of this group. The ingroup was represented by 65 species of the four recognized Heterothripidae genera (Aulacothrips Hood, Heterothrips Hood, Lenkothrips De Santis & Sureda, and Scutothrips Stannard). The monophyly of Heterothripidae was recovered in the total evidence and molecular data only analyses with the ectoparasitic Aulacothrips placed as the sister group of the remaining Heterothripidae. The large genus Heterothrips (>80% of the species-level diversity), which was thoroughly sampled in our analyses (56 species), was recovered as paraphyletic with respect to Scutothrips and Lenkothrips. We conclude that additional morphological and molecular data would be desirable before revising the classification of Heterothripidae

Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca)

2019 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y. W. Ho ◽  
Luana S. F. Lins ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Mantis Shrimp ◽  
Generic Groups ◽  
Morphological And Molecular Data

The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.

Total evidence phylogenetic analysis and reclassification ofEuschistusDallas within Carpocorini (Hemiptera: Pentatomidae: Pentatominae)

2016 ◽  
Vol 42 (2) ◽  
pp. 399-409 ◽  
Author(s):  
FILIPE M. BIANCHI ◽  
MARÍNDIA DEPRÁ ◽  
AUGUSTO FERRARI ◽  
JOCELIA GRAZIA ◽  
VERA L. S. VALENTE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Total Evidence

A total-evidence phylogenetic analysis of Hormaphidinae (Hemiptera: Aphididae), with comments on the evolution of galls

Cladistics ◽  
2013 ◽  
Vol 30 (1) ◽  
pp. 26-66 ◽  
Author(s):  
Jing Chen ◽  
Li-Yun Jiang ◽  
Ge-Xia Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Total Evidence
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