A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling

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Abstract

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer ( Odocoileini ) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama , Odocoileus , Pudu , M. americana , M. nemorivaga , Od. hemionus , and Od. virginianus . Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between “ Mazama ” pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis , and transfer pandora to Odocoileus . The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus . Pudu ( Pudu ) puda was not found sister to Pudu ( Pudella) mephistophiles . If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana , and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama , “ Mazama ” nemorivaga , and Hippocamelus antisensis . Noteworthy records that substantially extend the known distributions of M. temama and “ M. ” gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of “ M. ” nemorivaga , as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini .

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Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Martin Kircher, Susanna Sawyer, Matthias Meyer (2011)

Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.

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Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes.

Alexandre Hassanin, Frédéric Delsuc, Anne Ropiquet … (2012)

The order Cetartiodactyla includes cetaceans (whales, dolphins and porpoises) that are found in all oceans and seas, as well as in some rivers, and artiodactyls (ruminants, pigs, peccaries, hippos, camels and llamas) that are present on all continents, except Antarctica and until recent invasions, Australia. There are currently 332 recognized cetartiodactyl species, which are classified into 132 genera and 22 families. Most phylogenetic studies have focused on deep relationships, and no comprehensive time-calibrated tree for the group has been published yet. In this study, 128 new complete mitochondrial genomes of Cetartiodactyla were sequenced and aligned with those extracted from nucleotide databases. Our alignment includes 14,902 unambiguously aligned nucleotide characters for 210 taxa, representing 183 species, 107 genera, and all cetartiodactyl families. Our mtDNA data produced a statistically robust tree, which is largely consistent with previous classifications. However, a few taxa were found to be para- or polyphyletic, including the family Balaenopteridae, as well as several genera and species. Accordingly, we propose several taxonomic changes in order to render the classification compatible with our molecular phylogeny. In some cases, the results can be interpreted as possible taxonomic misidentification or evidence for mtDNA introgression. The existence of three new cryptic species of Ruminantia should therefore be confirmed by further analyses using nuclear data. We estimate divergence times using Bayesian relaxed molecular clock models. The deepest nodes appeared very sensitive to prior assumptions leading to unreliable estimates, primarily because of the misleading effects of rate heterogeneity, saturation and divergent outgroups. In addition, we detected that Whippomorpha contains slow-evolving taxa, such as large whales and hippos, as well as fast-evolving taxa, such as river dolphins. Our results nevertheless indicate that the evolutionary history of cetartiodactyls was punctuated by four main phases of rapid radiation during the Cenozoic era: the sudden occurrence of the three extant lineages within Cetartiodactyla (Cetruminantia, Suina and Tylopoda); the basal diversification of Cetacea during the Early Oligocene; and two radiations that involve Cetacea and Pecora, one at the Oligocene/Miocene boundary and the other in the Middle Miocene. In addition, we show that the high species diversity now observed in the families Bovidae and Cervidae accumulated mainly during the Late Miocene and Plio-Pleistocene. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

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Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

Brant C Faircloth, Travis Glenn (2012)

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (maxcount = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.

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Author and article information

Journal

Journal ID (nlm-ta): Zookeys

Journal ID (iso-abbrev): Zookeys

Journal ID (publisher-id): ZooKeys

Title: ZooKeys

Publisher: Pensoft Publishers

ISSN (Print): 1313-2989

ISSN (Electronic): 1313-2970

Publication date Collection: 2017

Publication date (Electronic): 14 September 2017

Issue: 697

Pages: 87-131

Affiliations

[1 ] PPG Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Av. Roraima n. 1000, Prédio 17, sala 1140-D, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brazil

[2 ] Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil

[3 ] Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC, USA

[4 ] Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA

[5 ] School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia

[6 ] Museum of Zoology, Senckenberg Natural History Collections, Dresden, Germany

[7 ] Instituto de Biología, Universidad Nacional Autónoma de México, circuito exterior s/n, Ciudad Universitaria, Coyoacán, CP04510, Mexico City, Mexico

[8 ] Integrative Research Center, Field Museum of Natural History, Chicago, IL60605, USA

[9 ] Environmental Science & Policy, George Mason University, 4400 University Dr., Fairfax, VA 22030, USA

Author notes

Corresponding author: Eliécer E. Gutiérrez ( gutierreze@ 123456si.edu )

Academic editor: Yasen Mutafchiev

Article

DOI: 10.3897/zookeys.697.15124

PMC ID: 5673856

SO-VID: cb4c226b-3a68-4a8b-978f-175256787a1b

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 17 July 2017

Date accepted : 30 August 2017

Funding

Funded by: Smithsonian Institution 100000014 http://doi.org/10.13039/100000014

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A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling

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Pensoft Biodiversity

Most cited references 122

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes.

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

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