ABSTRACT
A complete mitochondrial genome of Great Knot (Calidris tenuirostris), MK992912, was published by He and colleagues in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both C. tenuirostris (15,567 bp, 92.8%) and Pacific Golden Plover (Pluvialis fulva, 1208 bp, 7.2%). Detecting such errors is possible before publication if each sequenced fragment is separately analyzed phylogenetically before assembling the fragments into a single mitogenome. This mitogenome has been re-used in at least four phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
ABSTRACT
A recently published complete mitochondrial genome of Japanese or Temminck's cormorant (Phalacrocorax capillatus) was the first of this species (GenBank accession number LC714913). Comparison of COI sequences shows that this mitogenome clustered with great cormorant (Phalacrocorax carbo) rather than with its sister taxon P. capillatus. This suggests that the mitogenome was either a misidentified P. carbo or represents previously unknown intraspecific diversity in P. capillatus overlapping with that of P. carbo. Unfortunately, no voucher specimen was retained so it remains impossible to distinguish between these alternatives. We suggest that great restraint should be exercised using this mitogenome as a reference for P. capillatus. We reiterate previous pleas to retain voucher specimens for mitogenome sequences to enable re-analysis of the identity of the material.
ABSTRACT
A recently published complete mitochondrial genome of Spotted Greenshank (Tringa guttifer) was the first DNA sequence of this species (GenBank accession number MK905885, RefSeq number NC_044665; Liu et al. 2019, The complete mitochondrial genome of the Spotted Greenshank Tringa guttifer (Charadriiforemes [sic]: Charadriidae), Mitochondrial DNA Part B. 4:2353-2354). Here we show that this mitogenome is actually a chimera containing DNA fragments of both a Tringa sandpiper (presumably T. guttifer) and the Red-necked Stint (Calidris ruficollis). This mitogenome has been re-used in at least three phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
ABSTRACT
Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.
Subject(s)
Genome, Mitochondrial , Animals , Biological Evolution , Birds/genetics , Phylogeny , Phylogeography , Sequence Analysis, DNAABSTRACT
The recently published mitogenome of milk shark Rhizoprionodon acutus (MN602076/NC_046016) was fully resolved in an unexpected phylogenetic position in the original mitogenome announcement, which rendered the genus Scoliodon paraphyletic. Here, we show that this mitogenome is actually that of a misidentified Pacific spadenose shark (Scoliodon macrorhynchos). The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
ABSTRACT
The mitogenome of Eptesicus serotinus (Serotine bat) was published in 2013 with GenBank accession number KF111725 and NCBI Reference Sequence number NC_022474. This sequence was placed with Vespertilio sinensis (Asian parti-colored bat) in a COI gene tree but with Hypsugo alashanicus (Alashanian pipistrelle) in a cytochrome b gene tree. Direct comparison of mitogenomes showed that 92.4% of this mitogenome is similar to Vespertilio sinensis, 5.9% to Hypsugo alaschanicus, and that 1.6% of the mitogenome could not be attributed to either species, or any other species. This mitogenome has been re-used in at least 17 phylogenies. Our findings suggest that mitogenomes are best verified with multiple gene trees, followed by direct comparison of sequences. We conclude that greater vigilance is warranted to ensure that problematic sequences do not enter the scientific record, and are not re-used in subsequent studies.
ABSTRACT
Aruba, located close to the coasts of Colombia and Venezuela, is one of the most densely populated islands in the Caribbean and supports a wide range of marine-related socio-economic activities. However, little is known about the impacts of human activities on the marine environment. Injuries in marine mammals can be used to examine interactions with human activities and identify potential threats to the survival of populations. The prevalence of external injuries and tooth rake marks were examined in Atlantic spotted dolphin (Stenella frontalis) (nâ=â179), bottlenose dolphin (Tursiops truncatus) (nâ=â76) and false killer whale (Pseudorca crassidens) (nâ=â71) in Aruban waters using photo identification techniques. Eleven injury categories were defined and linked to either human-related activities or natural causes. All injury categories were observed. In total, 18.7% of all individuals had at least one injury. Almost half (41.7%) of the injuries could be attributed to human interactions, of which fishing gear was the most common cause (53.3%) followed by propeller hits (13.3%). Major disfigurements were observed in all three species and could be attributed to interactions with fishing gear. The results of this study indicate that fishing gear and propeller hits may pose threats to small and medium-sized cetaceans in Aruban waters. Thus, long-term monitoring of population trends is warranted. Shark-inflicted bite wounds were observed in Atlantic spotted dolphin and bottlenose dolphin. Bite wounds of cookie cutter sharks (Isistius sp.) were recorded in all three species, and include the first documented record of a cookie cutter shark bite in Atlantic spotted dolphin. This is one of the few studies which investigates the prevalence of injuries in cetaceans in the Caribbean. Further study is necessary to determine to which extent the injuries observed in Aruba affect the health and survival of local populations.
