Karl Kjer
University of Minnesota, Entomology, Graduate Student
- University of California, Davis, Entomology and Nematology, Faculty MemberRutgers, The State University of New Jersey, Ecology, Evolution, and Natural Resources, Faculty Memberadd
- Molecular systematist, now freelance science editor at Upworkedit
Research Interests: Evolutionary Biology, Zoology, Biology, Paraphyly, Odonata, and 3 moreMonophyly, Anisoptera, and Libellulidae
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Trnsient expression of a heat‐shock protein‐chloramphenicol acteyltrans‐Perase (hsp‐CAT) recombinant plasmid was used to define the parameters that influence transfection of cultured mosquito cells using DNA‐calcium phosphate... more
Trnsient expression of a heat‐shock protein‐chloramphenicol acteyltrans‐Perase (hsp‐CAT) recombinant plasmid was used to define the parameters that influence transfection of cultured mosquito cells using DNA‐calcium phosphate coprecipitates. The efficiency of the calcium phosphate procedure was strongly influenced by the growth state of recipient cells, and by the temperature at which the coprecipitate was prepared. Under optimal conditions, which included formation of the DNA‐calcium phosphate coprecipitate at 50°C, transfection frequencies were up to tenfold higher than those obtained using the previously described polybrene procedure.
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Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Previous phylogenetic hypotheses and progress on our ongoing data collection are summarized. Fragments of the... more
Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Previous phylogenetic hypotheses and progress on our ongoing data collection are summarized. Fragments of the large and small subunit nuclear ribosomal RNAs (D1, D3, V4–5), the nuclear elongation factor 1 alpha gene and a fragment of mitochondrial cytochrome oxidase 1 (COI) were sequenced, and molecular data were combined with previously published morphological data. Equally and differentially weighted parsimony analyses were conducted in order to present a phylogeny of Trichoptera, including 43 of 45 families. Our phylogeny closely resembles that proposed by Herbert Ross with respect to the relationships among suborders, with a monophyletic Annulipalpia at the base of the tree, and a clade consisting of Spicipalpia plus a monophyletic Integripalpia. The monophyly of Spicipalpia is weakly supported in the combined equally weighted analysis, and Spicipalpia is paraphyletic in the differentially weighted analysis. Within Integripalpia, our phylogeny recovered monophyletic Plenitentoria, Brevitentoria and Sericostomatoidea. Leptoceroidea was unresolved in the equally weighted analysis and monophyletic in the differentially weighted analysis. Within Annulipalpia, we recovered a basal but paraphyletic Philopotamoidea and a monophyletic Hydropsychoidea.
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Proceedings of the 1st Dresden Meeting of Insect Phylogeny. Dresden, September 19-12, 2003
Research Interests: Phylogenetics and Biology
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The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was... more
The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morphological characters. Both parsimony and mixed-model Bayesian likelihood analyses were performed. Under both methods, the mitochondrial and nuclear partitions support the same backbone phylogeny, as do the combined data. The utility of the molecular data is contrasted with the low phylogenetic signal among morphological characters. The phylogeny was used to trace the evolution of the host-plant association in Trirhabda. The recovered phylogeny shows that although the host-plant association is phylogenetically conservative, Trirhabda experienced one shift to a distantly related host-plant family, 6 shifts between host-plant tribes, and 6 between genera within tribes. The phylogeny reveals that Trirhabda were plesiomorphically adapted to tolerate complex secondary compounds of its host plants and this adaptation is retained in Trirhabda species, as evidenced by multiple shifts from chemically simpler host plants back to the more complex host plants.
Research Interests: Evolutionary Biology, Genetics, Geography, Phylogenetics, Molecular Evolution, and 15 moreBiology, Medicine, DNA, Animals, Molecular Phylogenetics and Evolution, Genus, Morphological Characters, Molecular phylogenetics, Beetles, Cell nucleus, Phylogenetic Tree, Bayes Theorem, Likelihood Functions, Host Plant, and Molecular Sequence Data
Research Interests: Evolutionary Biology, Microbiology, Phylogenetics, Molecular Evolution, Photosynthesis, and 15 moreMedical Microbiology, Biology, Medicine, Phylogeny, Maximum Likelihood, Animals, Secondary Structure, Monophyly, LSU rDNA, Maximum Parsimony, Base Sequence, Nucleic Acid Conformation, Euglena, Molecular Sequence Data, and Taxon
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Research Interests: Evolutionary Biology, Genetics, Systematic Biology, Phylogenetics, Biology, and 15 moreMedicine, Phylogeny, Sequence alignment, Animals, Insects, Secondary Structure, Monophyly, Phylogenetic Tree, Maximum Parsimony, Bayes Theorem, S, Likelihood Functions, Molecular Sequence Data, Nucleotide sequence, and Taxon
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Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and... more
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects
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The Trichoptera barcode of life initiative has gathered barcodes for a large portion of Trichoptera species diversity. Although the primary use of these data is species identification, they can also be used to generate species-level... more
The Trichoptera barcode of life initiative has gathered barcodes for a large portion of Trichoptera species diversity. Although the primary use of these data is species identification, they can also be used to generate species-level phylogenetic hypotheses. In order to ameliorate the well-documented difficulties of resolving deep divergences with the COI barcode fragment, we used a method of defining well-supported nodes from other data sources and filling out the “leaves” within these defined nodes of the Trichoptera tree of life with trees generated from the barcode fragment. We demonstrate the potential of this approach with the generation of a tree for Xiphocentronidae + Psychomyiidae. Using this example, we present two suspicious clades that warranted a more careful analysis, and demonstrate that a simple analysis of barcodes can generate and help answer other, related questions. We find that Zelandoptila is supported as belonging to Ecnomidae rather than Psychomyiidae, and we placed an unidentified specimen from the Smithsonian National Museum of Natural History collection as sister to Beraeidae.
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A phylogeny of Anisoptera employing 510 representatives of 184 genera (of ca. 380) in 11 families is presented based on an analysis of over 10,000 nucleotides from portions of the large and small subunit nuclear and mitochondrial... more
A phylogeny of Anisoptera employing 510 representatives of 184 genera (of ca. 380) in 11 families is presented based on an analysis of over 10,000 nucleotides from portions of the large and small subunit nuclear and mitochondrial ribosomal RNA’s, the mitochondrial protein coding genes COI and COII, and portions of the nuclear protein coding genes EF-1α and Histone H3. Ribosomal sequences were structurally aligned and sequences carefully checked to eliminate alignment errors, contamination, misidentification and paralogous gene amplicons. Both the RAxML and Bayesian topology based on consolidation of data at the generic level is ((Austropetaliidae, Aeshnidae), ((Gomphidae, Petaluridae), ((Chlorogomphidae, (Neopetaliidae, Cordulegastridae)), (Synthemistidae, (Macromiidae, (Corduliidae, Libellulidae)))))). As the positions of Petaluridae, Chlorogomphidae, Neopetaliidae, and Cordulegastridae are weakly supported, possible alternative hypotheses are discussed. New taxonomic groups establ...
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'Triplectides Australis' Navas, a leptocerid species reported in 1917 from a single specimen but not collected since, and 'Oxyethira albiceps' (McLachlan), the microcaddisfly species reported here, are the only caddisflies... more
'Triplectides Australis' Navas, a leptocerid species reported in 1917 from a single specimen but not collected since, and 'Oxyethira albiceps' (McLachlan), the microcaddisfly species reported here, are the only caddisflies ever recorded from Norfolk Island. This impoverished trichopteran fauna is discussed and compared with the notably endemic faunas of Lord Howe Island and New Caledonia, the two other major islands on the Norfolk Ridge of the southwestern Pacific. Comparisons of COI data confirm the initial morphology-based identification of the Norfolk Island microcaddisfly as a New Zealand species.
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We present our current phylogenetic hypothesis on the phylogeny of Trichoptera, generated from an analysis of over 7000 nucleotides from 18S and 28S rRNA, EF-1α, COI, and CAD. We corroborate our earlier hypotheses, with results that... more
We present our current phylogenetic hypothesis on the phylogeny of Trichoptera, generated from an analysis of over 7000 nucleotides from 18S and 28S rRNA, EF-1α, COI, and CAD. We corroborate our earlier hypotheses, with results that include a monophyletic Annulipalpia, Integripalpia, Brevitentoria, and Plenitentoria. Monophyly of Psychomyioidea, Pseudoneureclipsidae, and Grumichellinae were confirmed. The "Spicipalpian" families were again found to be paraphyletic, and most closely related to Integripalpia. Ptilocolepidae was not found to be monophyletic, but support for its paraphyly was so weak that we interpret our results as unresolved. We interpret our measures of branch support, and present a collapsed phylogeny that more conservatively represents our current hypothesis. We discuss how these data can eventually be merged into other sources of data, such as COI barcode data and transcriptomes, and suggest that a single huge analysis of all data, with all taxa, is unne...
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Research Interests: Phylogenetics and Biology
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they... more
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous sp...
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The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when... more
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985–2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a...
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Hymenoptera (sawflies, wasps, ants, and bees) are one of four mega-diverse insect orders, comprising more than 153,000 described and possibly up to one million undescribed extant species [1, 2]. As parasitoids, predators, and pollinators,... more
Hymenoptera (sawflies, wasps, ants, and bees) are one of four mega-diverse insect orders, comprising more than 153,000 described and possibly up to one million undescribed extant species [1, 2]. As parasitoids, predators, and pollinators, Hymenoptera play a fundamental role in virtually all terrestrial ecosystems and are of substantial economic importance [1, 3]. To understand the diversification and key evolutionary transitions of Hymenoptera, most notably from phytophagy to parasitoidism and predation (and vice versa) and from solitary to eusocial life, we inferred the phylogeny and divergence times of all major lineages of Hymenoptera by analyzing 3,256 protein-coding genes in 173 insect species. Our analyses suggest that extant Hymenoptera started to diversify around 281 million years ago (mya). The primarily ectophytophagous sawflies are found to be monophyletic. The species-rich lineages of parasitoid wasps constitute a monophyletic group as well. The little-known, species-poo...
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ABSTRACT Phylogenetic analysis was performed on a set of 242 morphological characters. The taxon sample included 31 Libellula, and representative species from selected libeluline tribes, from all libellulid subfamilies, from all... more
ABSTRACT Phylogenetic analysis was performed on a set of 242 morphological characters. The taxon sample included 31 Libellula, and representative species from selected libeluline tribes, from all libellulid subfamilies, from all libelluloid families, from all anisopteran superfamilies, and Epiophlebia. Cor-duliinae was shown to be paraphyletic even among genera characterized by a well developed anal loop bisector. Sympetrini was found to be polyphyletic with Crocothemis the sister group to Libel-lulini. The traditional placement of Trameini, far from Libellulini is in doubt, because it is here placed as the sister group to Crocothemis + Libellulini. Kennedy's phylogeny of Libellula was largely corroborated, with the following exceptions: the subgenera Libellula, Eolibellula, and Syn-tetrum form a monophyletic group which is the sister group to a clade including Belonia, Holota-nia, Neotetrum, and Eotainia subgenus nov. [type species Mesothemis composita Hagen]; and Eurothemis is determined to be the sister group of Ladona instead of Neotetrum. In addition we confirm Belonia to be monophyletic, and find Platetrum + Plathemis to form a monophyletic group, sister to Ladona + Eurothemis; these four subgenera together form the sister group to Libel-lula sensu stricto (s.s.).
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The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was... more
The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morphological characters. Both parsimony and mixed-model Bayesian likelihood analyses were performed. Under both methods, the mitochondrial and nuclear partitions support the same backbone phylogeny, as do the combined data. The utility of the molecular data is contrasted with the low phylogenetic signal among morphological characters. The phylogeny was used to trace the evolution of the host-plant association in Trirhabda. The recovered phylogeny shows that although the host-plant association is phylogenetically conservative, Trirhabda experienced one shift to a distantly related host-plant family, 6 shifts between host-plant tribes, and 6 between genera within tribes. The phylogeny reveals that Trirhabda were plesiomorphically adapted to tolerate complex secondary compounds of its host plants and this adaptation is retained in Trirhabda species, as evidenced by multiple shifts from chemically simpler host plants back to the more complex host plants.
Research Interests: Evolutionary Biology, Genetics, Zoology, Geography, Molecular Evolution, and 15 moreDNA, Phylogeny, United States, Animals, Polymerase Chain Reaction, Host-parasite interactions, Molecular Phylogenetics and Evolution, Morphological Characters, Beetles, Cell nucleus, Bayes Theorem, Likelihood Functions, Host Plant, Plant Leaves, and Molecular Sequence Data
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ABSTRACT The genus Chimarra (Trichoptera, Philopotamidae) is a cosmopolitan genus with over 700 species. The taxonomic history of Chimarra is discussed, with reference to how large genera are best subdivided. We also examine the... more
ABSTRACT The genus Chimarra (Trichoptera, Philopotamidae) is a cosmopolitan genus with over 700 species. The taxonomic history of Chimarra is discussed, with reference to how large genera are best subdivided. We also examine the phylogenetic utility of the COI "barcode" fragment and find it to be phylogenetically useful, within limits. Adding a single fragment of nuclear rRNA (specifically the 28S D2 region) converts the barcode hypothesis into a strongly supported phylogeny that is corroborated by a morphologically derived subgeneric classification. This suggests that a simple two gene dataset could be combined with morphological data in order to rapidly and inexpensively include a molecular component to generic revisions. We confirm the monophyly of Chimarra (Chimarra), C. (Curgia), C. (Otarrha), and core C. (Chimarrita). The C. (C.) tsudai group is also recovered. We make use of web-based materials, including the BOLD website (http:// www.boldsystems.org/), and keyhole markup language files (.kml format), which permit specimen data to be viewed on Google Earth. We suggest that static phylogenies presented in print could be dynamically updated with the use of these web materials.
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Transient expression of a heat-shock protein-chloramphenicol acetyltransferase (hsp-CAT) recombinant plasmid was used to define the parameters that influence transfection of cultured mosquito cells using DNA-calcium phosphate... more
Transient expression of a heat-shock protein-chloramphenicol acetyltransferase (hsp-CAT) recombinant plasmid was used to define the parameters that influence transfection of cultured mosquito cells using DNA-calcium phosphate coprecipitates. The efficiency of the calcium phosphate procedure was strongly influenced by the growth state of recipient cells, and by the temperature at which the coprecipitate was prepared. Under optimal conditions, which included formation of the DNA-calcium phosphate coprecipitate at 50 degrees C, transfection frequencies were up to tenfold higher than those obtained using the previously described polybrene procedure.
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Trophophoresy is exhibited in two ant genera: Acropyga (Formicinae), in which all 37 species are thought to be trophophoretic, and Tetraponera (Pseudomyrmecinae), in which it has been observed in only one species, T. binghami. This study... more
Trophophoresy is exhibited in two ant genera: Acropyga (Formicinae), in which all 37 species are thought to be trophophoretic, and Tetraponera (Pseudomyrmecinae), in which it has been observed in only one species, T. binghami. This study analyses a dataset comprised of both morphological and molecular (D2 region of 28S rRNA and EF1-alpha) data. Evidence is presented in favor of Acropyga being monophyletic, hence trophophoresy has evolved only once within the Formicinae and twice within the ants overall. The data further suggests that Acropyga belongs within a clade containing Anoplolepis, Aphomomyrmex, and Petalomyrmex. Aphomomyrmex and Petalomyrmex were found to be the sister group to Acropyga. The results indicate that the Lasiini and Plagiolepidini are not monophyletic and are in need of reexamination. Given the extant pantropical distribution of Acropyga it is speculated that Acropyga maybe of Gondwanan origin and that trophobiosis was the first form of agriculture to evolve in the ants.
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Biodiversity analyses based on Next Generation Sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering... more
Biodiversity analyses based on Next Generation Sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (> 99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www .1kite . org). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proport...
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The purpose of this paper is to explore relationships among frogs that have been (variously) placed in the Ranoidea. Phylogenetic analyses were conducted on data sets including 10 morphological characters and sequences from portions of... more
The purpose of this paper is to explore relationships among frogs that have been (variously) placed in the Ranoidea. Phylogenetic analyses were conducted on data sets including 10 morphological characters and sequences from portions of the 12S, 16S, and tRNA(val) mitochondrial genome. The resulting phylogenetic trees suggest that (1) the sooglossids are the sister group to all other microhyloid and ranoid frogs, (2) the Microhylidae may be the sister group of the Hyperoliidae, (3) the Hyperoliidae as classically defined may be diphyletic, (4) Hemisus appears to be a microhylid, and (4) the mantelline frogs may be clustered within the Rhacophoridae. Analysis shows that both morphological and molecular characters contain significant phylogenetic signal. Nonetheless, more morphological and molecular characters will be necessary to resolve completely the relationships among the deep branches of the Ranoidea.
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Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a... more
Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a "roachoid" fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.
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Abstract: The larval forms of most Chinese caddisflies remain undescribed. Hydropsychids deserve very high priority for associating larvae and adults because of their great diversity and biomass in aquatic ecosystems. The conventional... more
Abstract: The larval forms of most Chinese caddisflies remain undescribed. Hydropsychids deserve very high priority for associating larvae and adults because of their great diversity and biomass in aquatic ecosystems. The conventional approaches to associating larvae with adults include larval rearing and morphological identification of pharate adults. Progress in both methods has been very slow because of the strict microhabitat, diet and water chemistry requirements of the larvae and the rarity of pharate adults. A molecular approach using DNA fragments of both nuclear 28S ribosomal DNA (D2 fragment) and mitochondrial COI is developed for fast and reliable species delimitation and larva-adult association. Species boundaries are delimited based on the congruence between male morphology and phylograms constructed from independent gene sequences. Associations are made with reference to a phylogenetic analysis under two criteria: sequence identity between larvae and adults across both...
Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components... more
Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of t...
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>Abstract Computer alignments have been said to be more objective... more
>Abstract Computer alignments have been said to be more objective and repeatable than manual alignments. Here we suggest,that computer alignment methods, particularly those using a program called POY, suffer from a series of practical problems, and philosophical inconsistencies.Subjective decisions are still a part of POY analyses, but are less transparent. Wepoint out the problems POY has with ancestral state reconstruction