151
|
Haase M, Zielske S. Five new cryptic freshwater gastropod species from New Caledonia (Caenogastropoda, Truncatelloidea, Tateidae). Zookeys 2015:63-87. [PMID: 26478699 PMCID: PMC4602297 DOI: 10.3897/zookeys.523.6066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/28/2015] [Indexed: 11/12/2022] Open
Abstract
During the course of a project aiming at the reconstruction of the colonization of the South Pacific islands by tateid gastropods based on molecular data we discovered five new species on New Caledonia belonging to the genera Hemistomia and Leiorhagium, respectively. We describe these species based on morphological, anatomical and genetic data. All five species are morphologically cryptic as they closely resemble or are even indistinguishable from known species stressing the importance of a comprehensive taxonomic approach integrating several methods. As a consequence of their small and fragmented geographic ranges and the rapidly progressing anthropogenic land cover changes on New Caledonia, all five species qualify as critically endangered according to the criteria of the IUCN.
Collapse
Affiliation(s)
- Martin Haase
- Vogelwarte, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstraße 23, D-17489 Greifswald, Germany
| | - Susan Zielske
- Vogelwarte, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstraße 23, D-17489 Greifswald, Germany
| |
Collapse
|
152
|
Pepato AR, Klimov PB. Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment. BMC Evol Biol 2015; 15:178. [PMID: 26330076 PMCID: PMC4557820 DOI: 10.1186/s12862-015-0458-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites. RESULTS Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona. CONCLUSIONS Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.
Collapse
Affiliation(s)
- A R Pepato
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, Brazil.
| | - P B Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA.
- Tyumen State University, 10 Semakova St, Tyumen, 625003, Russia.
| |
Collapse
|
153
|
Bocakova M, Bocak L, Gimmel ML, Motyka M, Vogler AP. Aposematism and mimicry in soft-bodied beetles of the superfamily Cleroidea (Insecta). ZOOL SCR 2015. [DOI: 10.1111/zsc.12132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Milada Bocakova
- Department of Biology; Faculty of Education; Palacky University; Zizkovo nam. 5 CZ-771 40 Olomouc Czech Republic
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 CZ-771 46 Olomouc Czech Republic
| | - Ladislav Bocak
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 CZ-771 46 Olomouc Czech Republic
| | - Matthew L. Gimmel
- Department of Biology; Faculty of Education; Palacky University; Zizkovo nam. 5 CZ-771 40 Olomouc Czech Republic
| | - Michal Motyka
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 CZ-771 46 Olomouc Czech Republic
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot Berkshire SL5 7PY UK
| |
Collapse
|
154
|
Janssen T, Vizoso DB, Schulte G, Littlewood DTJ, Waeschenbach A, Schärer L. The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes. Mol Phylogenet Evol 2015; 92:82-107. [PMID: 26093054 DOI: 10.1016/j.ympev.2015.06.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/11/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022]
Abstract
The Macrostomorpha-an early branching and species-rich clade of free-living flatworms-is attracting interest because it contains Macrostomum lignano, a versatile model organism increasingly used in evolutionary, developmental, and molecular biology. We elucidate the macrostomorphan molecular phylogeny inferred from both nuclear (18S and 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40 representatives. Although our phylogeny does not recover the Macrostomorpha as a statistically supported monophyletic grouping, it (i) confirms many taxa previously proposed based on morphological evidence, (ii) permits the first placement of many families and genera, and (iii) reveals a number of unexpected placements. Specifically, Myozona and Bradynectes are outside the three classic families (Macrostomidae, Microstomidae and Dolichomacrostomidae) and the asexually fissioning Myomacrostomum belongs to a new subfamily, the Myozonariinae nov. subfam. (Dolichomacrostomidae), rather than diverging early. While this represents the first evidence for asexuality among the Dolichomacrostomidae, we show that fissioning also occurs in another Myozonariinae, Myozonaria fissipara nov. sp. Together with the placement of the (also fissioning) Microstomidae, namely as the sister taxon of Dolichomacrostomidae, this suggests that fissioning is not basal within the Macrostomorpha, but rather restricted to the new taxon Dolichomicrostomida (Dolichomacrostomidae+Microstomidae). Furthermore, our phylogeny allows new insights into the evolution of the reproductive system, as ancestral state reconstructions reveal convergent evolution of gonads, and male and female genitalia. Finally, the convergent evolution of sperm storage organs in the female genitalia appears to be linked to the widespread occurrence of hypodermic insemination among the Macrostomorpha.
Collapse
Affiliation(s)
- Toon Janssen
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| | - Dita B Vizoso
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Gregor Schulte
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, University Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | | | - Andrea Waeschenbach
- Natural History Museum, Life Sciences Department, Cromwell Rd, London SW7 5BD, UK
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| |
Collapse
|
155
|
Smith JPS, Litvaitis MK, Gobert S, Uyeno T, Artois T. Evolution and Functional Morphology of the Proboscis in Kalyptorhynchia (Platyhelminthes). Integr Comp Biol 2015; 55:205-16. [PMID: 26002347 DOI: 10.1093/icb/icv056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Predatory flatworms belonging to the taxon Kalyptorhynchia are characterized by an anterior muscular proboscis that they use to seize prey. In many cases, the proboscis is armed with hooks, derived either from the extracellular matrix that surrounds the muscles or from intracellular deposits in the epithelium covering the proboscis. Glands associated with the proboscis reportedly are venomous; however, there are few direct tests of this hypothesis. This article reviews the structure and current knowledge of the function of the proboscis in the Kalyptorhynchia, points to areas in which the current understanding of phylogenetic relationships within this taxon is incongruent with our hypothesis of how the proboscis evolved, and addresses areas in need of further research, especially as regards functional morphology and biomechanics.
Collapse
Affiliation(s)
- Julian P S Smith
- *Department of Biology, Winthrop University, Rock Hill, SC 29733, USA;
| | - Marian K Litvaitis
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Stefan Gobert
- Center for Environmental Sciences, Hasselt University, Hasselt 3500 Belgium
| | - Theodore Uyeno
- Department of Biology, Valdosta State University, Valdosta, GA 31698, USA
| | - Tom Artois
- Center for Environmental Sciences, Hasselt University, Hasselt 3500 Belgium
| |
Collapse
|
156
|
Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. Genome Biol Evol 2015; 7:1590-601. [PMID: 25977457 PMCID: PMC4494064 DOI: 10.1093/gbe/evv090] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.
Collapse
Affiliation(s)
- Ying Chang
- Department of Botany, University of British Columbia, Vancouver, British Columbia
| | - Sishuo Wang
- Department of Botany, University of British Columbia, Vancouver, British Columbia
| | - Satoshi Sekimoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, Chiba, Japan
| | | | - Cindy Choi
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, California
| | | | | | - Chew Yee Ngan
- DOE Joint Genome Institute, Walnut Creek, California
| | - Robin A Ohm
- DOE Joint Genome Institute, Walnut Creek, California
| | | | | | | | - Mary L Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia
| |
Collapse
|
157
|
Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
Collapse
Affiliation(s)
- Nathan V Whelan
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - Kenneth M Halanych
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
| |
Collapse
|
158
|
Golombek A, Tobergte S, Struck TH. Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes). Mol Phylogenet Evol 2015; 86:49-63. [DOI: 10.1016/j.ympev.2015.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/18/2015] [Accepted: 02/17/2015] [Indexed: 01/06/2023]
|
159
|
Zielske S, Haase M. Molecular phylogeny and a modified approach of character-based barcoding refining the taxonomy of New Caledonian freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae). Mol Phylogenet Evol 2015; 89:171-81. [PMID: 25929789 DOI: 10.1016/j.ympev.2015.04.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/11/2015] [Accepted: 04/21/2015] [Indexed: 11/26/2022]
Abstract
The islands of New Caledonia represent one of the world's biodiversity hotspots with many endemic species including freshwater gastropods of the family Tateidae. A phylogenetic analysis based on the mitochondrial COI and 16S rRNA and the nuclear ITS2 genes revealed two cryptic genera, Crosseana gen. n. and Novacaledonia gen. n. In order to provide character-based diagnoses we modified a DNA barcoding approach identifying strings of pairwise diagnostic characters, i.e. alignment positions, at which two genera are alternatively fixed for different nucleotides. The combination or string of all pairwise diagnostic characters was unique for each genus. Inconsistent mitochondrial and nuclear topologies suggest that Hemistomia cockerelli Haase and Bouchet, 1998 and H. fabrorum Haase and Bouchet, 1998, two morphologically well-defined species, hybridize. The age of the most recent common ancestor of the New Caledonian radiation of Tateidae was estimated at 24.6±9.5 MY. These findings are in line with the notion that New Caledonia is rather a Darwinian island that was colonized after an extended phase of submergence - in case of the tateids probably from Australia - despite being a fragment of Gondwanaland.
Collapse
Affiliation(s)
- Susan Zielske
- Vogelwarte, Zoological Institute and Museum, Greifswald University, Soldmannstr. 23, 17489 Greifswald, Germany.
| | - Martin Haase
- Vogelwarte, Zoological Institute and Museum, Greifswald University, Soldmannstr. 23, 17489 Greifswald, Germany.
| |
Collapse
|
160
|
Sela I, Ashkenazy H, Katoh K, Pupko T. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res 2015; 43:W7-14. [PMID: 25883146 PMCID: PMC4489236 DOI: 10.1093/nar/gkv318] [Citation(s) in RCA: 484] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/28/2015] [Indexed: 12/25/2022] Open
Abstract
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
Collapse
Affiliation(s)
- Itamar Sela
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Kazutaka Katoh
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| |
Collapse
|
161
|
Herman JL, Novák Á, Lyngsø R, Szabó A, Miklós I, Hein J. Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics 2015; 16:108. [PMID: 25888064 PMCID: PMC4395974 DOI: 10.1186/s12859-015-0516-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the alignment used, and neglecting the uncertainty in the alignment can lead to significant bias in the resulting inference. In recent years, a number of approaches have been developed for probabilistic sampling of alignments, rather than simply generating a single optimum. However, this type of probabilistic information is currently not widely used in the context of downstream inference, since most existing algorithms are set up to make use of a single alignment. RESULTS In this work we present a framework for representing a set of sampled alignments as a directed acyclic graph (DAG) whose nodes are alignment columns; each path through this DAG then represents a valid alignment. Since the probabilities of individual columns can be estimated from empirical frequencies, this approach enables sample-based estimation of posterior alignment probabilities. Moreover, due to conditional independencies between columns, the graph structure encodes a much larger set of alignments than the original set of sampled MSAs, such that the effective sample size is greatly increased. CONCLUSIONS The alignment DAG provides a natural way to represent a distribution in the space of MSAs, and allows for existing algorithms to be efficiently scaled up to operate on large sets of alignments. As an example, we show how this can be used to compute marginal probabilities for tree topologies, averaging over a very large number of MSAs. This framework can also be used to generate a statistically meaningful summary alignment; example applications show that this summary alignment is consistently more accurate than the majority of the alignment samples, leading to improvements in downstream tree inference. Implementations of the methods described in this article are available at http://statalign.github.io/WeaveAlign .
Collapse
Affiliation(s)
- Joseph L Herman
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.
- Division of Mathematical Biology, National Institute of Medical Research,, The Ridgeway, London, NW7 1AA, UK.
| | - Ádám Novák
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.
| | - Rune Lyngsø
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.
| | - Adrienn Szabó
- Institute of Computer Science and Control, Hungarian Academy of Sciences, Lagymanyosi u. 11., Budapest, 1111, Hungary.
| | - István Miklós
- Institute of Computer Science and Control, Hungarian Academy of Sciences, Lagymanyosi u. 11., Budapest, 1111, Hungary.
- Department of Stochastics, Rényi Institute, Reáltanoda u. 13-15, Budapest, 1053, Hungary.
| | - Jotun Hein
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.
| |
Collapse
|
162
|
The phylogenetic utility of acetyltransferase (ARD1) and glutaminyl tRNA synthetase (QtRNA) for reconstructing Cenozoic relationships as exemplified by the large Australian cicada Pauropsalta generic complex. Mol Phylogenet Evol 2015; 83:258-77. [DOI: 10.1016/j.ympev.2014.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 06/25/2014] [Accepted: 07/14/2014] [Indexed: 11/19/2022]
|
163
|
Gasmi S, Nève G, Pech N, Tekaya S, Gilles A, Perez Y. Evolutionary history of Chaetognatha inferred from molecular and morphological data: a case study for body plan simplification. Front Zool 2014; 11:84. [PMID: 25473413 PMCID: PMC4254178 DOI: 10.1186/s12983-014-0084-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/30/2014] [Indexed: 11/18/2022] Open
Abstract
Background Chaetognatha are a phylum of marine carnivorous animals which includes more than 130 extant species. The internal systematics of this group have been intensively debated since it was discovered in the 18th century. While they can be traced back to the earlier Cambrian, they are an extraordinarily homogeneous phylum at the morphological level - a fascinating characteristic that puzzled many a scientist who has tried to clarify their taxonomy. Recent studies which have attempted to reconstruct a phylogeny using molecular data have relied on single gene analyses and a somewhat restricted taxon sampling. Here, we present the first large scale phylogenetic study of Chaetognatha based on a combined analysis of nearly the complete ribosomal RNA (rRNA) genes. We use this analysis to infer the evolution of some morphological characters. This work includes 36 extant species, mainly obtained from Tara Oceans Expedition 2009/2012, that represent 16 genera and 6 of the 9 extant families. Results Cladistic and phenetic analysis of morphological characters, geometric morphometrics and molecular small subunit (SSU rRNA) and large subunit (LSU rRNA) ribosomal genes phylogenies provided new insights into the relationships and the evolutionary history of Chaetognatha. We propose the following clade structure for the phylum: (((Sagittidae, Krohnittidae), Spadellidae), (Eukrohniidae, Heterokrohniidae)), with the Pterosagittidae included in the Sagittidae. The clade (Sagittidae, Krohnittidae) constitutes the monophyletic order of Aphragmophora. Molecular analyses showed that the Phragmophora are paraphyletic. The Ctenodontina/Flabellodontina and Syngonata/Chorismogonata hypotheses are invalidated on the basis of both morphological and molecular data. This new phylogeny also includes resurrected and modified genera within Sagittidae. Conclusions The distribution of some morphological characters traditionally used in systematics and for species diagnosis suggests that the diversity in Chaetognatha was produced through a process of mosaic evolution. Moreover, chaetognaths have mostly evolved by simplification of their body plan and their history shows numerous convergent events of losses and reversions. The main morphological novelty observed is the acquisition of a second pair of lateral fins in Sagittidae, which represents an adaptation to the holoplanktonic niche. Electronic supplementary material The online version of this article (doi:10.1186/s12983-014-0084-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samah Gasmi
- Aix-Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13331 Marseille cedex 3, France ; Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES12 Biologie de la Reproduction et du Développement animal, 2092 El Manar, Tunis Tunisie
| | - Gabriel Nève
- Aix-Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13331 Marseille cedex 3, France
| | - Nicolas Pech
- Aix-Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13331 Marseille cedex 3, France
| | - Saïda Tekaya
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES12 Biologie de la Reproduction et du Développement animal, 2092 El Manar, Tunis Tunisie
| | - André Gilles
- Aix-Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13331 Marseille cedex 3, France
| | - Yvan Perez
- Aix-Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13331 Marseille cedex 3, France
| |
Collapse
|
164
|
Cannon JT, Kocot KM, Waits DS, Weese DA, Swalla BJ, Santos SR, Halanych KM. Phylogenomic resolution of the hemichordate and echinoderm clade. Curr Biol 2014; 24:2827-32. [PMID: 25454590 DOI: 10.1016/j.cub.2014.10.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 02/01/2023]
Abstract
Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans.
Collapse
Affiliation(s)
- Johanna T Cannon
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Department of Zoology, Naturhistoriska Riksmuseet, 104 05 Stockholm, Sweden; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA.
| | - Kevin M Kocot
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA
| | - Damien S Waits
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA
| | - David A Weese
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA
| | - Billie J Swalla
- Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA
| | - Scott R Santos
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA.
| |
Collapse
|
165
|
Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspock U, Aspock H, Bartel D, Blanke A, Berger S, Bohm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schutte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TKF, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science 2014; 346:763-7. [DOI: 10.1126/science.1257570] [Citation(s) in RCA: 1672] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
166
|
Meyer-Wachsmuth I, Curini Galletti M, Jondelius U. Hyper-cryptic marine meiofauna: species complexes in Nemertodermatida. PLoS One 2014; 9:e107688. [PMID: 25225981 PMCID: PMC4166464 DOI: 10.1371/journal.pone.0107688] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/08/2014] [Indexed: 01/30/2023] Open
Abstract
Nemertodermatida are microscopically small, benthic marine worms. Specimens of two nominal species, Sterreria psammicola and Nemertinoides elongatus from 33 locations worldwide were sequenced for three molecular markers. Species delimitation and validation was done using gene trees, haplotype networks and multilocus Bayesian analysis. We found 20 supported species of which nine: Nemertinoides glandulosum n.sp., N. wolfgangi n.sp., Sterreria boucheti n.sp., S. lundini n.sp., S. martindalei n.sp., S. monolithes n.sp., S. papuensis n.sp., S. variabilis n.sp. and S. ylvae n.sp., are described including nucleotide-based diagnoses. The distribution patterns indicate transoceanic dispersal in some of the species. Sympatric species were found in many cases. The high level of cryptic diversity in this meiofauna group implies that marine diversity may be higher than previously estimated.
Collapse
Affiliation(s)
- Inga Meyer-Wachsmuth
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Marco Curini Galletti
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| |
Collapse
|
167
|
Misof B, Meusemann K, von Reumont BM, Kück P, Prohaska SJ, Stadler PF. A priori assessment of data quality in molecular phylogenetics. Algorithms Mol Biol 2014. [DOI: 10.1186/s13015-014-0022-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
168
|
Hering L, Mayer G. Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in panarthropoda. Genome Biol Evol 2014; 6:2380-91. [PMID: 25193307 PMCID: PMC4202329 DOI: 10.1093/gbe/evu193] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/17/2023] Open
Abstract
Screening of a deeply sequenced transcriptome using Illumina sequencing as well as the genome of the tardigrade Hypsibius dujardini revealed a set of five opsin genes. To clarify the phylogenetic position of these genes and to elucidate the evolutionary history of opsins in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we reconstructed the phylogeny of broadly sampled metazoan opsin genes using maximum likelihood and Bayesian inference methods in conjunction with carefully selected substitution models. According to our findings, the opsin repertoire of H. dujardini comprises representatives of all three major bilaterian opsin clades, including one r-opsin, three c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of the tardigrade ortholog of neuropsin/opsin-5 is the first record of this opsin type in a protostome, but our screening of available metazoan genomes revealed that it is also present in other protostomes. Our opsin phylogeny further suggests that two r-opsins, including an "arthropsin," were present in the last common ancestor of Panarthropoda. Although both r-opsin lineages were retained in Onychophora and Arthropoda, the arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin found in H. dujardini supports the hypothesis of monochromatic vision in the panarthropod ancestor, whereas two duplications of the ancestral panarthropod c-opsin have led to three c-opsins in tardigrades. Although the early-branching nodes are unstable within the metazoans, our findings suggest that the last common ancestor of Bilateria possessed six opsins: Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go opsin) was lost in the ecdysozoan lineage.
Collapse
Affiliation(s)
- Lars Hering
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Germany
| | - Georg Mayer
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Germany
| |
Collapse
|
169
|
Kück P, Meid SA, Groß C, Wägele JW, Misof B. AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support. BMC Bioinformatics 2014; 15:294. [PMID: 25176556 PMCID: PMC4167143 DOI: 10.1186/1471-2105-15-294] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/14/2014] [Indexed: 01/14/2023] Open
Abstract
Background Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree. Results We used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The approach implemented in AliGROOVE allows to detect nodes within a tree that are supported despite the absence of phylogenetic signal in the underlying multiple sequence alignment. We show that AliGROOVE equally well detects heterogeneous sequence divergence in a case study based on an empirical data set of mitochondrial DNA sequences of chelicerates. Conclusions The AliGROOVE approach has the potential to identify single taxa or subsets of taxa which show predominantly randomized sequence similarity in comparison with other taxa in a multiple sequence alignment. It further allows to evaluate the reliability of node support in a novel way. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-294) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Patrick Kück
- Zoologisches Forschungsmuseum A, Koenig, Adenauerallee 160-163, 53113 Bonn, Germany.
| | | | | | | | | |
Collapse
|
170
|
Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc Biol Sci 2014; 281:20140970. [PMID: 24966318 PMCID: PMC4083801 DOI: 10.1098/rspb.2014.0970] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/04/2014] [Indexed: 11/12/2022] Open
Abstract
Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.
Collapse
Affiliation(s)
- Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
171
|
O'Hara TD, Hugall AF, Thuy B, Moussalli A. Phylogenomic resolution of the class Ophiuroidea unlocks a global microfossil record. Curr Biol 2014; 24:1874-9. [PMID: 25065752 DOI: 10.1016/j.cub.2014.06.060] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/23/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
Our understanding of the origin, evolution, and biogeography of seafloor fauna is limited because we have insufficient spatial and temporal data to resolve underlying processes. The abundance and wide distribution of modern and disarticulated fossil Ophiuroidea, including brittle stars and basket stars, make them an ideal model system for global marine biogeography if we have the phylogenetic framework necessary to link extant and fossil morphology in an evolutionary context. Here we construct a phylogeny from a highly complete 425-gene, 61-taxa transcriptome-based data set covering 15 of the 18 ophiuroid families and representatives of all extant echinoderm classes. We calibrate our phylogeny with a series of novel fossil discoveries from the early Mesozoic. We confirm the traditional paleontological view that ophiuroids are sister to the asteroids and date the crown group Ophiuroidea to the mid-Permian (270 ± 30 mega-annum). We refute all historical classification schemes of the Ophiuroidea based on gross structural characters but find strong congruence with schemes based on lateral arm plate microstructure and the temporal appearance of various plate morphologies in the fossil record. The verification that these microfossils contain phylogenetically informative characters unlocks their potential to advance our understanding of marine biogeographical processes.
Collapse
Affiliation(s)
| | - Andrew F Hugall
- Museum Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Ben Thuy
- Section Paléontologie, Musée National d'Histoire Naturelle du Luxembourg, 24 Rue Münster, 2160 Luxembourg
| | - Adnan Moussalli
- Museum Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| |
Collapse
|
172
|
Tessens B, Janssen T, Artois T. Molecular phylogeny of Kalyptorhynchia (Rhabdocoela, Platyhelminthes) inferred from ribosomal sequence data. ZOOL SCR 2014. [DOI: 10.1111/zsc.12066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Bart Tessens
- Centre for Environmental Sciences; Hasselt University; Martelarenlaan 42 Hasselt 3500 Belgium
| | - Toon Janssen
- Research Unit Nematology; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Tom Artois
- Centre for Environmental Sciences; Hasselt University; Martelarenlaan 42 Hasselt 3500 Belgium
| |
Collapse
|
173
|
Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CKC, Chen W, Lopker KB. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics 2014; 15:230. [PMID: 24990571 PMCID: PMC4227113 DOI: 10.1186/1471-2105-15-230] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/29/2014] [Indexed: 01/09/2023] Open
Abstract
Background Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis. Results We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/). Conclusions Osiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.
Collapse
Affiliation(s)
- Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
| | | | | | | | | | | | | |
Collapse
|
174
|
Timmermans MJTN, Lees DC, Simonsen TJ. Towards a mitogenomic phylogeny of Lepidoptera. Mol Phylogenet Evol 2014; 79:169-78. [PMID: 24910155 DOI: 10.1016/j.ympev.2014.05.031] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/11/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae.
Collapse
Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
| | - David C Lees
- Department of Zoology, Cambridge University, Downing Street CB2 3EJ, United Kingdom.
| | - Thomas J Simonsen
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| |
Collapse
|
175
|
Redelings B. Erasing errors due to alignment ambiguity when estimating positive selection. Mol Biol Evol 2014; 31:1979-93. [PMID: 24866534 DOI: 10.1093/molbev/msu174] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Current estimates of diversifying positive selection rely on first having an accurate multiple sequence alignment. Simulation studies have shown that under biologically plausible conditions, relying on a single estimate of the alignment from commonly used alignment software can lead to unacceptably high false-positive rates in detecting diversifying positive selection. We present a novel statistical method that eliminates excess false positives resulting from alignment error by jointly estimating the degree of positive selection and the alignment under an evolutionary model. Our model treats both substitutions and insertions/deletions as sequence changes on a tree and allows site heterogeneity in the substitution process. We conduct inference starting from unaligned sequence data by integrating over all alignments. This approach naturally accounts for ambiguous alignments without requiring ambiguously aligned sites to be identified and removed prior to analysis. We take a Bayesian approach and conduct inference using Markov chain Monte Carlo to integrate over all alignments on a fixed evolutionary tree topology. We introduce a Bayesian version of the branch-site test and assess the evidence for positive selection using Bayes factors. We compare two models of differing dimensionality using a simple alternative to reversible-jump methods. We also describe a more accurate method of estimating the Bayes factor using Rao-Blackwellization. We then show using simulated data that jointly estimating the alignment and the presence of positive selection solves the problem with excessive false positives from erroneous alignments and has nearly the same power to detect positive selection as when the true alignment is known. We also show that samples taken from the posterior alignment distribution using the software BAli-Phy have substantially lower alignment error compared with MUSCLE, MAFFT, PRANK, and FSA alignments.
Collapse
Affiliation(s)
- Benjamin Redelings
- Biology Department, Duke UniversityThe National Evolutionary Synthesis Center, Durham, NC
| |
Collapse
|
176
|
Rehm P, Meusemann K, Borner J, Misof B, Burmester T. Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing. Mol Phylogenet Evol 2014; 77:25-33. [PMID: 24732681 DOI: 10.1016/j.ympev.2014.04.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 02/02/2023]
Abstract
Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.
Collapse
Affiliation(s)
- Peter Rehm
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany; CSIRO Ecosystem Sciences, Australian National Insect Collection, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Janus Borner
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany
| | - Thorsten Burmester
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany.
| |
Collapse
|
177
|
Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ. Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3. Syst Biol 2014; 63:645-59. [DOI: 10.1093/sysbio/syu027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Derrick J. Zwickl
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| | - Joshua C. Stein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| | - Rod A. Wing
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| | - Doreen Ware
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| | - Michael J. Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and 4Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| |
Collapse
|
178
|
Peters RS, Meusemann K, Petersen M, Mayer C, Wilbrandt J, Ziesmann T, Donath A, Kjer KM, Aspöck U, Aspöck H, Aberer A, Stamatakis A, Friedrich F, Hünefeld F, Niehuis O, Beutel RG, Misof B. The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol 2014; 14:52. [PMID: 24646345 PMCID: PMC4000048 DOI: 10.1186/1471-2148-14-52] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 03/04/2014] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups. RESULTS In our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees. CONCLUSIONS Our phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult's flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.
Collapse
Affiliation(s)
- Ralph S Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Adenauerallee 160, 53113 Bonn, Germany
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
- CSIRO Ecosystem Sciences, Australian National Insect Collection, Clunies Ross Street, Acton ACT 2601, Australia
| | - Malte Petersen
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Christoph Mayer
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Jeanne Wilbrandt
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Tanja Ziesmann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Alexander Donath
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Karl M Kjer
- Rutgers University, Department of Ecology, Evolution and Natural Resources, New Brunswick, NJ 08901, USA
| | - Ulrike Aspöck
- Naturhistorisches Museum Wien, 2. Zool. Abteilung, Burgring 7, 1010 Vienna, Austria
- Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Horst Aspöck
- Institut für Spezifische Prophylaxe und Tropenmedizin, Medizinische Parasitologie, Medizinische Universität Wien (MUW), Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Andre Aberer
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Karlsruher Institut für Technologie, Fakultät für Informatik, Postfach 698076128 Karlsruhe, Germany
| | - Frank Friedrich
- Biozentrum Grindel und Zoologisches Museum Hamburg, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Frank Hünefeld
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstraße. 1, 07743 Jena, Germany
| | - Oliver Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| | - Rolf G Beutel
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstraße. 1, 07743 Jena, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany
| |
Collapse
|
179
|
Resch MC, Shrubovych J, Bartel D, Szucsich NU, Timelthaler G, Bu Y, Walzl M, Pass G. Where taxonomy based on subtle morphological differences is perfectly mirrored by huge genetic distances: DNA barcoding in Protura (Hexapoda). PLoS One 2014; 9:e90653. [PMID: 24609003 PMCID: PMC3946556 DOI: 10.1371/journal.pone.0090653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Protura is a group of tiny, primarily wingless hexapods living in soil habitats. Presently about 800 valid species are known. Diagnostic characters are very inconspicuous and difficult to recognize. Therefore taxonomic work constitutes an extraordinary challenge which requires special skills and experience. Aim of the present pilot project was to examine if DNA barcoding can be a useful additional approach for delimiting and determining proturan species. Methodology and Principal Findings The study was performed on 103 proturan specimens, collected primarily in Austria, with additional samples from China and Japan. The animals were examined with two markers, the DNA barcoding region of the mitochondrial COI gene and a fragment of the nuclear 28S rDNA (Divergent Domain 2 and 3). Due to the minuteness of Protura a modified non-destructive DNA-extraction method was used which enables subsequent species determination. Both markers separated the examined proturans into highly congruent well supported clusters. Species determination was performed without knowledge of the results of the molecular analyses. The investigated specimens comprise a total of 16 species belonging to 8 genera. Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0–21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%). Conclusions The study clearly demonstrates that the tricky morphological taxonomy in Protura has a solid biological background and that accurate species delimitation is possible using both markers, COI and 28S rDNA. The fact that both molecular and morphological analyses can be performed on the same individual will be of great importance for the description of new species and offers a valuable new tool for biological and ecological studies, in which proturans have generally remained undetermined at species level.
Collapse
Affiliation(s)
- Monika Carol Resch
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Julia Shrubovych
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Daniela Bartel
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Nikolaus U. Szucsich
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
- * E-mail:
| | - Gerald Timelthaler
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Yun Bu
- Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Manfred Walzl
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Günther Pass
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| |
Collapse
|
180
|
Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, Minh BQ, von Haeseler A, Ebersberger I, Pass G, Misof B. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol 2014; 31:239-49. [PMID: 24140757 PMCID: PMC3879454 DOI: 10.1093/molbev/mst196] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.
Collapse
Affiliation(s)
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
- CSIRO Ecosystem Sciences, Australian National Insect Collection, Acton, ACT, Australia
| | | | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Benjamin Meyer
- Institut für Systemische Neurowissenschaften, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Janus Borner
- Biozentrum Grindel & Zoologisches Museum, Universität Hamburg, Hamburg, Germany
| | - Malte Petersen
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| | - Andre J. Aberer
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
- Karlsruher Institut für Technologie, Fakultät für Informatik, Karlsruhe, Germany
| | - Manfred G. Walzl
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Ingo Ebersberger
- Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Günther Pass
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| |
Collapse
|
181
|
Kocot KM, Halanych KM, Krug PJ. Phylogenomics supports Panpulmonata: Opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs. Mol Phylogenet Evol 2013; 69:764-71. [DOI: 10.1016/j.ympev.2013.07.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 06/11/2013] [Accepted: 07/01/2013] [Indexed: 12/17/2022]
|
182
|
Cannon JT, Swalla BJ, Halanych KM. Hemichordate molecular phylogeny reveals a novel cold-water clade of harrimaniid acorn worms. THE BIOLOGICAL BULLETIN 2013; 225:194-204. [PMID: 24445445 DOI: 10.1086/bblv225n3p194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hemichordates are instrumental to understanding early deuterostome and chordate evolution, yet diversity and relationships within the group have been understudied. Recently, there has been renewed interest in hemichordate diversity and taxonomy, although current findings suggest that much hemichordate diversity remains to be discovered. Herein, we present a molecular phylogenetic study based on nuclear 18S rDNA sequence data, which includes 35 previously unsampled taxa and represents all recognized hemichordate families. We include mitochondrial 16S rDNA data from 66 enteropneust taxa and three pterobranch Rhabdopleura species, and recover colonial pterobranchs and solitary enteropneusts as reciprocally monophyletic taxa. Our phylogenetic results also reveal a previously unknown clade of at least four species of harrimaniid enteropneusts from cold waters, including Antarctica, the North Atlantic around Iceland and Norway, and the deep sea off Oregon. These small worms (1-5 mm in length), occur from 130 to 2950 m and are not closely related to other deep-sea harrimaniids, indicating that diversity of enteropneusts within the deep sea is broader than previously described in the literature. Discovery of this clade, as well as larger torquaratorids from Antarctica, strengthens hypotheses of close associations between Antarctic and deep-sea fauna.
Collapse
Affiliation(s)
- Johanna T Cannon
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, Alabama 36849
| | | | | |
Collapse
|
183
|
Lemmon EM, Lemmon AR. High-Throughput Genomic Data in Systematics and Phylogenetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135822] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, Florida 32306;
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida 32306;
| |
Collapse
|
184
|
The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). BIOMED RESEARCH INTERNATIONAL 2013; 2013:407072. [PMID: 24350268 PMCID: PMC3856133 DOI: 10.1155/2013/407072] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 08/08/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022]
Abstract
Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.
Collapse
|
185
|
Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B. New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol 2013; 13:253. [PMID: 24238092 PMCID: PMC4225663 DOI: 10.1186/1471-2148-13-253] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/07/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity. RESULTS The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata. CONCLUSION Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.
Collapse
Affiliation(s)
- Maximilian P Nesnidal
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| | - Martin Helmkampf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Achim Meyer
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Alexander Witek
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str 74, D-20359 Hamburg, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Str 13, D-60438 Frankfurt, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Torsten H Struck
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D-53113 Bonn, Germany
| | - Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| |
Collapse
|
186
|
Bonato L, Drago L, Murienne J. Phylogeny of Geophilomorpha (Chilopoda) inferred from new morphological and molecular evidence. Cladistics 2013; 30:485-507. [DOI: 10.1111/cla.12060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Lucio Bonato
- Dipartimento di Biologia; Università di Padova; Padova Italy
| | - Leandro Drago
- Dipartimento di Biologia; Università di Padova; Padova Italy
| | - Jérôme Murienne
- CNRS; Université Paul Sabatier; ENFA; UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique); Université de Toulouse; Toulouse France
| |
Collapse
|
187
|
Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
Collapse
Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
188
|
Corse E, Rampal J, Cuoc C, Pech N, Perez Y, Gilles A. Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data. PLoS One 2013; 8:e59439. [PMID: 23593138 PMCID: PMC3625178 DOI: 10.1371/journal.pone.0059439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy.
Collapse
Affiliation(s)
- Emmanuel Corse
- IMBE (UMR CNRS 7263, IRD 237) Evolution Génome Environnement, Aix-Marseille Université, Marseille, France.
| | | | | | | | | | | |
Collapse
|
189
|
Mitochondrial genomes to the rescue--Diurodrilidae in the myzostomid trap. Mol Phylogenet Evol 2013; 68:312-26. [PMID: 23563272 DOI: 10.1016/j.ympev.2013.03.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 11/20/2022]
Abstract
Diurodrilidae is a taxon of Lophotrochozoa comprising about six, exclusively interstitial species, which are up to 500μm long and dorsoventrally flattened. Traditionally, Diurodrilidae had been regarded as an annelid family. However, recently Diurodrilidae had been excluded from Annelida and been placed in closer relationship to platyzoan taxa based on both morphological and nuclear rRNA data. Since both, Diurodrilidae and platyzoan taxa, exhibit long branches in the molecular analyses, the close relationship might be due to a long branch attraction artifact. The annelid taxon Myzostomida had been trapped in a similar long branch attraction artifact with platyzoan taxa using nuclear rRNA data, but determination of the nearly complete mitochondrial genome of myzostomids revealed their annelid affinity. Therefore, we determined the nearly complete mitochondrial genome of Diurodrilus subterraneus as well as new nuclear rRNA data for D. subterraneus and some platyzoan taxa. All our analyses of nuclear rRNA and mitochondrial sequence and gene order data presented herein clearly place Diurodrilidae within Annelida and with strong nodal support values in some analyses. Therefore, the previously suggested exclusion of Diurodrilidae from Annelida and its close relationship with platyzoan taxa can be attributed to a long branch artifact. Morphological data do not unambiguously support a platyzoan affinity of Diurodrilidae, but instead would also be in line with a progenetic origin of Diurodrilidae within Annelida.
Collapse
|
190
|
Van Steenkiste N, Tessens B, Willems W, Backeljau T, Jondelius U, Artois T. A comprehensive molecular phylogeny of dalytyphloplanida (platyhelminthes: rhabdocoela) reveals multiple escapes from the marine environment and origins of symbiotic relationships. PLoS One 2013; 8:e59917. [PMID: 23536894 PMCID: PMC3607561 DOI: 10.1371/journal.pone.0059917] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/20/2013] [Indexed: 11/18/2022] Open
Abstract
In this study we elaborate the phylogeny of Dalytyphloplanida based on complete 18S rDNA (156 sequences) and partial 28S rDNA (125 sequences), using a Maximum Likelihood and a Bayesian Inference approach, in order to investigate the origin of a limnic or limnoterrestrial and of a symbiotic lifestyle in this large group of rhabditophoran flatworms. The results of our phylogenetic analyses and ancestral state reconstructions indicate that dalytyphloplanids have their origin in the marine environment and that there was one highly successful invasion of the freshwater environment, leading to a large radiation of limnic and limnoterrestrial dalytyphloplanids. This monophyletic freshwater clade, Limnotyphloplanida, comprises the taxa Dalyelliidae, Temnocephalida, and most Typhloplanidae. Temnocephalida can be considered ectosymbiotic Dalyelliidae as they are embedded within this group. Secondary returns to brackish water and marine environments occurred relatively frequently in several dalyeliid and typhloplanid taxa. Our phylogenies also show that, apart from the Limnotyphloplanida, there have been only few independent invasions of the limnic environment, and apparently these were not followed by spectacular speciation events. The distinct phylogenetic positions of the symbiotic taxa also suggest multiple origins of commensal and parasitic life strategies within Dalytyphloplanida. The previously established higher-level dalytyphloplanid clades are confirmed in our topologies, but many of the traditional families are not monophyletic. Alternative hypothesis testing constraining the monophyly of these families in the topologies and using the approximately unbiased test, also statistically rejects their monophyly.
Collapse
|
191
|
Wilke T, Haase M, Hershler R, Liu HP, Misof B, Ponder W. Pushing short DNA fragments to the limit: Phylogenetic relationships of ‘hydrobioid’ gastropods (Caenogastropoda: Rissooidea). Mol Phylogenet Evol 2013; 66:715-36. [DOI: 10.1016/j.ympev.2012.10.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 10/18/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
|
192
|
Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 2013. [DOI: 10.1016/j.ympev.2012.11.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
193
|
Nesnidal MP, Helmkampf M, Bruchhaus I, El-Matbouli M, Hausdorf B. Agent of whirling disease meets orphan worm: phylogenomic analyses firmly place Myxozoa in Cnidaria. PLoS One 2013; 8:e54576. [PMID: 23382916 PMCID: PMC3559788 DOI: 10.1371/journal.pone.0054576] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/12/2012] [Indexed: 12/15/2022] Open
Abstract
Myxozoa are microscopic obligate endoparasites with complex live cycles. Representatives are Myxobolus cerebralis, the causative agent of whirling disease in salmonids, and the enigmatic "orphan worm" Buddenbrockia plumatellae parasitizing in Bryozoa. Originally, Myxozoa were classified as protists, but later several metazoan characteristics were reported. However, their phylogenetic relationships remained doubtful. Some molecular phylogenetic analyses placed them as sister group to or even within Bilateria, whereas the possession of polar capsules that are similar to nematocysts of Cnidaria and of minicollagen genes suggest a close relationship between Myxozoa and Cnidaria. EST data of Buddenbrockia also indicated a cnidarian origin of Myxozoa, but were not sufficient to reject a closer relationship to bilaterians. Phylogenomic analyses of new genomic sequences of Myxobolus cerebralis firmly place Myxozoa as sister group to Medusozoa within Cnidaria. Based on the new dataset, the alternative hypothesis that Myxozoa form a clade with Bilateria can be rejected using topology tests. Sensitivity analyses indicate that this result is not affected by long branch attraction artifacts or compositional bias.
Collapse
Affiliation(s)
| | | | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | | |
Collapse
|
194
|
Powell AF, Barker FK, Lanyon SM. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study. Mol Phylogenet Evol 2013; 66:69-79. [DOI: 10.1016/j.ympev.2012.09.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 09/08/2012] [Accepted: 09/08/2012] [Indexed: 10/27/2022]
|
195
|
|
196
|
Rajan V. A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments. Mol Biol Evol 2012. [PMID: 23193120 DOI: 10.1093/molbev/mss264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.
Collapse
|
197
|
Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One 2012; 7:e49794. [PMID: 23185439 PMCID: PMC3501463 DOI: 10.1371/journal.pone.0049794] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
Collapse
Affiliation(s)
- László G Nagy
- University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
| | | | | | | | | | | | | |
Collapse
|
198
|
Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Mol Biol Evol 2012; 30:215-33. [DOI: 10.1093/molbev/mss216] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
199
|
Schwarzer J, Swartz ER, Vreven E, Snoeks J, Cotterill FPD, Misof B, Schliewen UK. Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution. Proc Biol Sci 2012; 279:4389-98. [PMID: 22951733 DOI: 10.1098/rspb.2012.1667] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.
Collapse
Affiliation(s)
- Julia Schwarzer
- Bavarian State Collection of Zoology, Münchhausenstrasse 21, Munich, Germany
| | | | | | | | | | | | | |
Collapse
|
200
|
Letsch HO, Meusemann K, Wipfler B, Schütte K, Beutel R, Misof B. Insect phylogenomics: results, problems and the impact of matrix composition. Proc Biol Sci 2012; 279:3282-90. [PMID: 22628473 PMCID: PMC3385742 DOI: 10.1098/rspb.2012.0744] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/02/2012] [Indexed: 11/12/2022] Open
Abstract
In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.
Collapse
Affiliation(s)
- Harald O Letsch
- Department für Tropenökologie und Biodiversität der Tiere, Universität Wien, Rennweg 14, 1030 Wien, Austria.
| | | | | | | | | | | |
Collapse
|