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opencc-by-4.0Jul 2020View details →

Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf

Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf. Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. Journal of the Ocean Science Foundation, 35, 54–64.

opencc-zeroDec 2010View details →

Data from: Testicular melanization has evolved in birds with high mtDNA mutation rates

Melanin is mainly found in the integument of animals, but it also appears in several extracutaneous tissues. The presence of melanin in testes has been anecdotally reported in all vertebrate groups, but the causes and functions of this melanin remain unknown. Similar to other extracutaneous melanins, testicular melanin may protect male germ cells from oxidative stress. Given the high respiratory activity of spermatozoa, oxidative stress generated by mitochondrial dysfunction as a consequence of mtDNA mutations directly affects sperm viability. Thus, natural selection may favour testicular melanization in males of species with high historical mutation rates in the mitochondrial genome. Here, we tested this hypothesis using information on occurrence of testicular melanization and mutation accumulation as reflected by cytochrome b mtDNA base pair substitution rates in a large set of 134 species of birds, controlling for the confounding effects of body mass, reproductive activity and phylogeny. We found that testicular melanization has evolved in species with high rates of accumulated mitochondrial mutations and propose that this is an adaptive response related to the protective capacity of melanin against oxidative stress. In support of this hypothesis, testicular melanization was more frequently observed during the breeding season of birds (i.e. when spermatogenesis is likely to occur) than during reproductive inactivity. In contrast to other extracutaneous melanins whose abundance seems to reflect skin and coat colour, we did not find a correlation between the proportion of plumage coloured by melanins and occurrence of testicular melanization. Whereas future experimental studies should test these hypotheses, our study highlights for the first time that melanization patterns in animals may evolve as a response to historical mutation rates.

opencc-zeroDec 2011View details →

Data from: Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey

Most species with lengthy migrations display some degree of natal homing; some (e.g., migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine microsatellite loci to examine population structure in 965 Pacific lamprey from 20 locations from central British Columbia to southern California, and supplemented this analysis with mitochondrial DNA restriction fragment length polymorphism analysis on a subset of 530 lamprey. Microsatellite analysis revealed: 1) relatively low but often statistically significant genetic differentiation among locations (97% pairwise FST values were less than 0.04 but 73.7% were significant); and 2) weak but significant isolation-by-distance (r2 = 0.0565, P = 0.0450) but no geographic clustering of samples. The few moderate FST values involved comparisons with sites that were geographically distant or far upstream. The mtDNA analysis—although providing less resolution among sites (only 4.7% FST values were significant)—was broadly consistent with the microsatellite results: 1) the southernmost site and some sites tributary to the Salish Sea were genetically distinct; and 2) southern sites showed higher haplotype and private haplotype richness. These results are inconsistent with philopatry, suggesting that anadromous lampreys are unusual among species with long migrations, but suggest that limited dispersal at sea precludes panmixia in this species.

opencc-zeroDec 2010View details →

Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.

opennotspecifiedDec 2016View details →

FIGURE 5 in Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations

FIGURE 5. Flightless Notaris sp. from Kazakhstan, V6165.

opencc-zeroOct 2023View details →

MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups. One such technocomplex where the maker is unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which covers an area in northwestern and central Europe from the UK to Poland. This paper presents the morphological and proteomic species identification, mitochondrial DNA analysis, and direct radiocarbon dating of human remains directly associated to an LRJ assemblage at the cave site of Ilsenhöhle in Ranis (Germany).

Figure 11. Elytral margin color and maculation. A. Cicindela d in A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies C. Barry Knisley

Figure 11. Elytral margin color and maculation. A. Cicindela d. bonnevillensis, female, "UT: Tooele County: Dugway Proving Grounds, 10-V-2009" (MGKC). B. Cicindela d. montevolans, female, "UT: Cache Co, Swan Flat Rd. W of Hwy 89, 19-VI-2010" (MGKC). C. Cicindela d. decemnotata, female,"MT: Broadwater Co., SE side Canyon Ferry Res., 7-V-2007" (MGKC). D. Cicindela d. decemnotata, male, "MT: Broadwater Co., Centennial Valley, 27 May 1999" (MGKC).

Figure 18. Genal setae. A. and B. C. d in A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies C. Barry Knisley

Figure 18. Genal setae. A. and B. C. d. decemnotata, male, "MT: Yellowstone Co., NE of Billings, 28-IV-2008" (MGKC). C. C. d. decemnotata, male, "MT: Beaverhead Co., Centennial Valley, 12-V-2007" (MGKC). D. C. d. meriwetheri, female, "WA: Walla Walla Co., Hwy 12 E of Hwy 730, 3-X-2003" (MGKC).

Figure 8. Cicindela d. bonnevillensis. A. and B in A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies C. Barry Knisley

Figure 8. Cicindela d. bonnevillensis. A. and B. Habitat and adults: Delle, Tooele Co., UT, 31-III-2011.

Figure 2. Cicindela d. decemnotata adult habitus. A in A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies C. Barry Knisley

Figure 2. Cicindela d. decemnotata adult habitus. A. Female, "MT: Beaverhead Co., Centennial Valley, 3-VI-2007" (MGKC). B. Male, "MT: Broadwater Co., SE of Canyon Ferry Res., 7-V-2007" (MGKC). C. Male, "CO: Larimer Co., Jct 15/88, 14-VI-1992" (CSUC). D. Male, "MT: Beaverhead Co., Centennial Valley, 27-VI-2009" (MGKC). E. Male, "CO: Montezuma Co., Mesa Verde N.P. 8-V-1999" (MGKC). F. Male, "CO: Park Co., Barlow Ranch, VI-1915" (MGKC). Scale bar = 5mm for all.

opencc-zeroFeb 2024View details →

Fejervarya mtDNA phylogenetics files

The Lesser Sunda Archipelago is one of the world's most tectonically complex regions and hosts a unique assemblage of amphibian species. Paddy frogs (genus Fejervarya) occur throughout the region, but the distribution of each constituent species remains unclear. We present a set of mtDNA sequence data on the three paddy frog species (or species complexes) in the Lesser Sundas, F. cancrivora, F. iskandari, and F. verruculosa. These data were analyzed with the Maximum Likelihood phylogenetic software IQTree as well as the Bayesian phylogenetic software BEAST2. The DNA alignments, results files, log files, and tree files are deposited here.

opennotspecifiedJan 2021View details →

Table 2 in Species boundaries and phylogeographic patterns in new species of Nannoniscus (Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology

Table 2. List of voucher specimens used for molecular-genetic analyses. All type specimens are located at the CeNak, Universität Hamburg (ZMH catalogue), while voucher specimens of undescribed species are located at the DZMB, Hamburg<table><tbody><tr><th>Voucher ID #</th><th>Voyage</th><th>Area</th><th>Station</th><th>Species</th><th>Marker</th><th>GenBank accession #</th><th>Collection #</th><th>Sex</th></tr></tbody><tbody><tr><th>Na43</th><td>AB02</td><td>OMS*</td><td>S11</td><td>Nannoniscus sp.</td><td>16S</td><td>MT259290</td><td>DZMB-69115</td><td>F</td></tr><tr><th>Na37</th><td>AB02</td><td>OMS</td><td>S11</td><td>Nannoniscus sp.</td><td>16S</td><td>MT259291</td><td>DZMB-69116</td><td>F</td></tr><tr><th>Na39</th><td>AB02</td><td>OMS</td><td>S11</td><td>Nannoniscus sp.</td><td>16S</td><td>MT259292</td><td>DZMB-69117</td><td>F</td></tr><tr><th>AB2ISO431</th><td>AB02</td><td>OMS</td><td>S5</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256412</td><td>DZMB-69118</td><td>F</td></tr><tr><th>AB2ISO442</th><td>AB02</td><td>UK</td><td>U7</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256413</td><td>DZMB-69119</td><td>M</td></tr><tr><th>Na41</th><td>AB02</td><td>OMS</td><td>S10</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256414</td><td>DZMB-69120</td><td>F</td></tr><tr><th>NB12_Iso020</th><td>BIONOD</td><td>GER</td><td>06</td><td>N. hilario</td><td>COI</td><td>KJ736105</td><td>ZMH K-55341</td><td>F</td></tr><tr><th>Na25</th><td>JPIO</td><td>GER PA</td><td>24</td><td>N. hilario</td><td>COI,</td><td>MT256415</td><td>ZMH K-55381</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259293</td><td></td><td></td></tr><tr><th>Na23</th><td>JPIO</td><td>GER PA</td><td>24</td><td>N. hilario</td><td>COI</td><td>MT256416</td><td>ZMH K-55342</td><td>F</td></tr><tr><th>NB12_Iso445</th><td>BIONOD</td><td>FRA</td><td>101</td><td>Nannoniscus sp.</td><td>COI</td><td>KJ736107</td><td>DZMB-69121</td><td>F</td></tr><tr><th>Na14</th><td>JPIO</td><td>FRA</td><td>158</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256417</td><td>DZMB-69124</td><td>F</td></tr><tr><th>NB12_Iso098</th><td>BIONOD</td><td>FRA</td><td>67</td><td>Nannoniscus sp.</td><td>COI</td><td>KJ736106</td><td>DZMB-69122</td><td>F</td></tr><tr><th>Na16</th><td>JPIO</td><td>FRA</td><td>158</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256418</td><td>DZMB-69125</td><td>M</td></tr><tr><th>Na20</th><td>JPIO</td><td>GSR</td><td>133</td><td>Nannoniscus sp.</td><td>COI,</td><td>MT256419</td><td>DZMB-69126</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259294</td><td></td><td></td></tr><tr><th>MA13_Iso453</th><td>MA13</td><td>GER PRZ</td><td>90</td><td>N. menoti</td><td>COI</td><td>MT256420</td><td>ZMH K-55348</td><td>F</td></tr><tr><th>Iso1005/Na40</th><td>AB02</td><td>OMS</td><td>S11</td><td>N. menoti</td><td>COI</td><td>MT256421</td><td>ZMH K-55349</td><td>F</td></tr><tr><th>MA14_Iso272</th><td>MA14</td><td>GER PRZ</td><td>38</td><td>N. menoti</td><td>COI</td><td>MT256422</td><td>ZMH K-55350</td><td>M</td></tr><tr><th>MA14_Iso352</th><td>MA14</td><td>GER PRZ</td><td>39</td><td>N. menoti</td><td>COI</td><td>MT256423</td><td>ZMH K-55351</td><td>F</td></tr><tr><th>Na06</th><td>JPIO</td><td>GSR</td><td>117</td><td>N. menoti</td><td>COI</td><td>MT256424</td><td>ZMH K-55352</td><td>F</td></tr><tr><th>NB12_Iso068</th><td>BIONOD</td><td>GER</td><td>33</td><td>N. menoti</td><td>COI</td><td>KJ736104</td><td>ZMH K-55353</td><td>F</td></tr><tr><th>Na27</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. menoti</td><td>COI,</td><td>MT256425</td><td>ZMH K-55354</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259295</td><td></td><td></td></tr><tr><th>Iso1120/Na42</th><td>AB02</td><td>APEI-6</td><td>APEI-6#1</td><td>N. menoti</td><td>COI</td><td>MT256426</td><td>ZMH K-55355</td><td>F</td></tr><tr><th>Na18</th><td>JPIO</td><td>GER PA</td><td>20</td><td>N. menoti</td><td>COI</td><td>MT256427</td><td>ZMH K-55356</td><td>F</td></tr><tr><th>MA13_Iso049</th><td>MA13</td><td>GER PA</td><td>07</td><td>N. pedro</td><td>COI</td><td>MT256428</td><td>ZMH K-55357</td><td>F</td></tr><tr><th>Na08</th><td>JPIO</td><td>GSR</td><td>133</td><td>N. pedro</td><td>COI,</td><td>MT256429</td><td>ZMH K-55358</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259296</td><td></td><td></td></tr><tr><th>MA13_Iso593</th><td>MA13</td><td>GER PRZ</td><td>90</td><td>N. pedro</td><td>COI</td><td>MT256430</td><td>ZMH K-55359</td><td>F</td></tr><tr><th>NB12_Iso290</th><td>BIONOD</td><td>GER</td><td>43</td><td>N. pedro</td><td>COI</td><td>KJ736102</td><td>ZMH K-55360</td><td>F</td></tr><tr><th>Na04</th><td>JPIO</td><td>GER PA</td><td>20</td><td>N. pedro</td><td>COI,</td><td>MT256431</td><td>ZMH K-55361</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259297</td><td></td><td></td></tr><tr><th>Na11</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. pedro</td><td>COI</td><td>MT256432</td><td>ZMH K-55362</td><td>F</td></tr><tr><th>Na22</th><td>JPIO</td><td>GER PA</td><td>24</td><td>N. pedro</td><td>COI</td><td>MT256433</td><td>ZMH K-55363</td><td>F</td></tr><tr><th>NB12_Iso330</th><td>BIONOD</td><td>GER</td><td>43</td><td>N. pedro</td><td>COI</td><td>KJ736103</td><td>ZMH K-55364</td><td>F</td></tr><tr><th>Na05</th><td>JPIO</td><td>GER PA</td><td>20</td><td>N. pedro</td><td>COI,</td><td>MT256434</td><td>ZMH K-55365</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259298</td><td></td><td></td></tr><tr><th>MA14_Iso242</th><td>MA14</td><td>GER PRZ</td><td>39</td><td>N. pedro</td><td>COI</td><td>MT256435</td><td>ZMH K-55366</td><td>M</td></tr><tr><th>MA14_Iso319</th><td>MA14</td><td>GER PRZ</td><td>39</td><td>N. pedro</td><td>COI</td><td>MT256436</td><td>ZMH K-55367</td><td>F</td></tr><tr><th>MA14_Iso258</th><td>MA14</td><td>GER IRZ</td><td>21</td><td>N. brenkei</td><td>COI</td><td>MT256437</td><td>ZMH K-55368</td><td>M?</td></tr><tr><th>Na03</th><td>JPIO</td><td>GER PA</td><td>20</td><td>N. brenkei</td><td>COI,</td><td>MT256438</td><td>ZMH K-55369</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259299</td><td></td><td></td></tr><tr><th>NB12_Iso070</th><td>BIONOD</td><td>GER</td><td>33</td><td>N. brenkei</td><td>COI</td><td>KJ736101</td><td>ZMH K-55370</td><td>F</td></tr><tr><th>Na24</th><td>JPIO</td><td>GER PA</td><td>24</td><td>N. brenkei</td><td>COI</td><td>MT256439</td><td>ZMH K-55371</td><td>F</td></tr><tr><th>Na21</th><td>JPIO</td><td>GER PA</td><td>24</td><td>Nannoniscus sp.</td><td>COI</td><td>MT256440</td><td>DZMB-69129</td><td>F</td></tr><tr><th>NB12_Iso099</th><td>BIONOD</td><td>FRA</td><td>67</td><td>N. magdae</td><td>COI</td><td>KJ736099</td><td>ZMH K-55373</td><td>F</td></tr><tr><th>Na12</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. magdae</td><td>COI</td><td>MT256441</td><td>ZMH K-55374</td><td>F</td></tr><tr><th>Na26</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. magdae</td><td>COI,</td><td>MT256442</td><td>ZMH K-55375</td><td>F</td></tr><tr><th></th><td></td><td></td><td></td><td></td><td>16S</td><td>MT259300</td><td></td><td></td></tr><tr><th>Na28</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. magdae</td><td>COI</td><td>MT256443</td><td>ZMH K-55376</td><td>F</td></tr><tr><th>Na49</th><td>JPIO</td><td>FRA</td><td>171</td><td>N. magdae</td><td>COI</td><td>MT256444</td><td>ZMH K-55377</td><td>M</td></tr><tr><th>Na19</th><td>JPIO</td><td>GER PA</td><td>20</td><td>Nannoniscus sp.</td><td>16S</td><td>MT271781</td><td>DZMB-69130</td><td>M</td></tr><tr><th>Na33</th><td>JPIO</td><td>FRA</td><td>158</td><td>Nannoniscus sp.</td><td>16S</td><td>MT259301</td><td>DZMB-69131</td><td>F</td></tr><tr><th>Na17</th><td>JPIO</td><td>FRA</td><td>158</td><td>Nannoniscus sp.</td><td>16S</td><td>MT259302</td><td>DZMB-69132</td><td>F</td></tr><tr><th>NB12_Iso303</th><td>BIONOD</td><td>GER</td><td>43</td><td>Nannoniscus sp. 4</td><td>COI</td><td>KJ736054</td><td>DZMB-69133</td><td></td></tr><tr><th>NB12_Iso310</th><td>BIONOD</td><td>GER</td><td>43</td><td>Nannoniscus sp. 4</td><td>COI</td><td>KJ736055</td><td>DZMB-69134</td><td></td></tr><tr><th>NB12_Iso307</th><td>BIONOD</td><td>GER</td><td>43</td><td>Nannoniscus sp. 4</td><td>COI</td><td>KJ736053</td><td>DZMB-69135</td><td></td></tr><tr><th>VTDesm013</th><td>VEMA</td><td>NEA</td><td>2–6</td><td>Ketosoma vemae</td><td>COI</td><td>MF040892</td><td>ZMH K-46140</td><td>M</td></tr><tr><th>D3D060</th><td>DIVA3</td><td>ARG</td><td>534</td><td>Ketosoma werneri</td><td>COI</td><td>MF040893</td><td>ZMH K-46142</td><td>F</td></tr><tr><th>NBIso337</th><td>BIONOD</td><td>GER</td><td>43</td><td>Ketosoma ruehlemanni</td><td>COI</td><td>KJ736158</td><td>ZMH K-46139</td><td>M</td></tr></tbody></table>*APEI: Area of Particular Environmental Interest, FRA: French licence area; GER: German licence area, GSR: G-TEC Sea Mineral Resources NV; OMS: Ocean Mineral Singapore Pte. Ltd.; UK: UK Seabed Resources Ltd.; IRZ: impact reference zone; PA, prospective mining area; PRZ: preservation reference zone; NEA: North-East Atlantic; Argentine basin; M: male, F: female.

opennotspecifiedJan 2021View details →

Table 1 in Species boundaries and phylogeographic patterns in new species of Nannoniscus (Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology

Table 1. Station list of CCZ sampling sites across where examined Nannoniscus specimens were collected [including gear type, date, position (degrees) and depth (m)]<table><tbody><tr><th>Voyage</th><th>Area</th><th>Gear</th><th>Station</th><th>Date</th><th>Start latitude °N</th><th>Start longitude °W</th><th>End latitude °N</th><th>End longitude °W</th><th>Depth (m)</th></tr></tbody><tbody><tr><th>AB02</th><td>OMS*</td><td>EBS</td><td>S10</td><td>2015-03-14</td><td>12°2’17.16’’</td><td>117°14’12’’</td><td>12°2’29’’</td><td>117°13’1’’</td><td>4097–4094</td></tr><tr><th>AB02</th><td>OMS</td><td>EBS</td><td>S11</td><td>2015-03-16</td><td>12°2’43.08’’</td><td>117°25’26’’</td><td>12°3’1.44’’</td><td>117°24’17’’</td><td>4223–4235</td></tr><tr><th>AB02</th><td>APEI-6</td><td>EBS</td><td>APEI-6#1</td><td>2015-03-20</td><td>19°27’52’’</td><td>120°1’31’’</td><td>19°28’54’’</td><td>120°0’58’’</td><td>4099–4076</td></tr><tr><th>AB02</th><td>OMS</td><td>EBS</td><td>S5</td><td>2015-03-01</td><td>12°15’3’’</td><td>117°19’14’’</td><td>n.a.</td><td>n.a.</td><td>4137</td></tr><tr><th>AB02</th><td>UK</td><td>EBS</td><td>U7</td><td>2015-03-02</td><td>12°27’5’’</td><td>116°37’48’’</td><td>n.a.</td><td>n.a.</td><td>4145</td></tr><tr><th>JPIO</th><td>GER PA</td><td>EBS</td><td>20</td><td>2015-03-21</td><td>11°50’9’’</td><td>117°58’29’’</td><td>11°50’11’’</td><td>116°58’0’’</td><td>4093</td></tr><tr><th>JPIO</th><td>GER PA</td><td>EBS</td><td>24</td><td>2015-03-22</td><td>11°51’19’’</td><td>117°1’30’’</td><td>11°51’31’’</td><td>116°58’0’’</td><td>4093</td></tr><tr><th>JPIO</th><td>GSR</td><td>EBS</td><td>117</td><td>2015-04-07</td><td>13°52’19’’</td><td>123°15’27’’</td><td>13°52’37’’</td><td>123°14’16’’</td><td>4498–4521</td></tr><tr><th>JPIO</th><td>GSR</td><td>EBS</td><td>133</td><td>2015-04-10</td><td>13°50’45’’</td><td>123°15’39’’</td><td>13°51’8’’</td><td>123°14’8’’</td><td>4516–4427</td></tr><tr><th>JPIO</th><td>FRA</td><td>EBS</td><td>158</td><td>2015-04-15</td><td>14°3’25’’</td><td>130°7’59’’</td><td>14°3’49’’</td><td>130°6’29’’</td><td>4946–4978</td></tr><tr><th>JPIO</th><td>FRA</td><td>EBS</td><td>171</td><td>2015-04-17</td><td>14°2’41’’</td><td>130°5’57’’</td><td>14°3’12’’</td><td>130°4’36’’</td><td>5024–5017</td></tr><tr><th>MA13</th><td>GER PA</td><td>EBS</td><td>07</td><td>2013-04-12</td><td>11°51’30.18’’</td><td>117°01’12.30’’</td><td>11°51’45.36’’</td><td>117°0’10.26’’</td><td>4131–4121</td></tr><tr><th>MA13</th><td>GER PRZ</td><td>EBS</td><td>90</td><td>2013-05-03</td><td>11°49’44.52’’</td><td>117°30’16.68’’</td><td>111°49’54.36’’</td><td>117°29’23.7’’</td><td>4340–4357</td></tr><tr><th>MA14</th><td>GER IRZ</td><td>EBS</td><td>20</td><td>2014-05-10</td><td>11°51’32’’</td><td>117°01’8’’</td><td>11°51’43’’</td><td>117°00’19’’</td><td>4127–4124</td></tr><tr><th>MA14</th><td>GER IRZ</td><td>EBS</td><td>21</td><td>2014-05-10</td><td>11°49’44.52’’</td><td>117°00’27.06’’</td><td>11°49’56.76’’</td><td>116°59’40.62’’</td><td>4132–4136</td></tr><tr><th>MA14</th><td>GER PRZ</td><td>EBS</td><td>38</td><td>2014-05-13</td><td>11°47’52’’</td><td>117°30’31’’</td><td>11°48’3’’</td><td>117°29’45’’</td><td>4363–4373</td></tr><tr><th>MA14</th><td>GER PRZ</td><td>EBS</td><td>39</td><td>2014-05-13</td><td>11°49’37’’</td><td>117°30’49’’</td><td>11°49’47’’</td><td>117°30’5’’</td><td>4361–4343</td></tr><tr><th>BIONOD</th><td>GER</td><td>EBS</td><td>06</td><td>2012-04-02</td><td>11°46’13’’</td><td>116°41’8’’</td><td>11°46’13’’</td><td>116°41’7’’</td><td>4259</td></tr><tr><th>BIONOD</th><td>GER</td><td>EBS</td><td>33</td><td>2012-04-07</td><td>11°51’44’’</td><td>117°3’10’’</td><td>11°51’54’’</td><td>117°3’8’’</td><td>4133</td></tr><tr><th>BIONOD</th><td>GER</td><td>EBS</td><td>43</td><td>2012-04-09</td><td>11°48’12’’</td><td>117°32’3’’</td><td>11°48’20’’</td><td>117°31’57.079’’</td><td>4358</td></tr><tr><th>BIONOD</th><td>FRA</td><td>EBS</td><td>67</td><td>2012-04-19</td><td>14°3’4’’</td><td>130°4’36’’</td><td>14°3’10’’</td><td>130°4’27’’</td><td>5021</td></tr><tr><th>BIONOD</th><td>FRA</td><td>EBS</td><td>101</td><td>2012-04-25</td><td>14°4’51’’</td><td>130° 6’11’’</td><td>14°5’0’’</td><td>130°6’11’’</td><td>5055</td></tr></tbody></table>*APEI: Area of Particular Environmental Interest; FRA: French licence area; GER: German licence area; GSR: G-TEC Sea Mineral Resources NV; OMS: Ocean Mineral Singapore Pte. Ltd.; UK: UK Seabed Resources Ltd.; IRZ: impact reference zone; PA, prospective mining area; PRZ: preservation reference zone.

opencc-by-4.0Jun 2017View details →

Figure 8 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies

Figure 8. Relationship of diagnosability to Nei's net nucleotide divergence (dA, Nei and Kumar 2000). Colors indicate taxonomic level of comparison: species (blue), subspecies (green), and populations (red). Vertical lines indicate the binomial 95% CI around diagnosability. Note that x-axis for dA is log10-scaled.

opencc-by-4.0Oct 2021View details →

Fig. 2 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico

Fig. 2. Maximum Likelihood gene tree (highest log: -3134.13), constructed with COI barcode sequences of Pseudocellus Platnick, 1980. Colors of the branches indicate species; same colors are in the bars, which represent the different species delimitation methods used for their validation. Red branches + red circle indicate the new species described herein. Numbers below the bars represent the number of species recovered under each species delimitation method (not considering the outgroup: Ricinoides feae (Hansen, 1921)): 1: morphology (M). 2: GMYC. 3: ABGD with recursive partitions (RP). 4: ABGD with initial partitions (IP). 5: bPTP with IB. 6: bPTP with ML. 7: ASAP. Numbers on the branches are Bootstrap support values (>50% significant).

opencc-by-4.0Oct 2021View details →

Figs 27–31 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico

Figs 27–31. Pseudocellus giribeti sp. nov. Paratype, ♀ (MCZ 80010). 27–28. Habitus, dorsal and ventral views. 29–31. Spermathecae, anterior, posterior and lateral views, respectively. Scale bars: 27–28 = 2 mm; 29–31 = 0.2 mm.

opencc-by-4.0Oct 2021View details →

Figs 11–19 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico

Figs 11–19. Pseudocellus giribeti sp. nov. Holotype, ♂ (MCZ 80010). 11. Cucullus, dorsal view. 12. Left chelicera, dorsal view. 13–14. Right tibia II, prolateral and proventral views. 15–16. Right metatarsus II, prolateral and proventral views. 17. Right femur II, prolateral view. 18. Detail of the movable and fixed claws of the right pedipalp, retrolateral view. 19. Right pedipalp tibia, retrolateral view. Scale bars: 11, 13–17, 19 = 0.5 mm; 12 = 0.2 mm; 18 = 0.1 mm.

opencc-zeroJun 2022View details →

Zapus hudsonius luteus microsatellite and mtDNA datasets

In the face of accelerated warming and drying, habitat specialists of riparian zones could be threatened with genetic erosion if their effective population sizes become small due to loss and fragmentation of habitat. The New Mexico meadow jumping mouse (Zapus hudsonius luteus) is Endangered due to a suite of disturbances to their riparian habitat but the degree of functional connectivity within and among the drainages they occupy is unknown. Using microsatellite and mtDNA, we examined the hypothesis of hydrologically-mediated gene flow (via riparian networks) by assessing structure, diversity, and the possibility of overland dispersal among disconnected watersheds (White Mountains, AZ). Both a priori and de novo structure supported stream-mediated gene flow. However, inferred clusters crossed watershed boundaries, and migration rates and dispersers suggest infrequent use of overland paths at nearby sub-drainages among each watershed. Analysis of mtDNA indicated that this was likely a long-term phenomenon, also suggesting that one of the watersheds (LCR) may have been more historically diverse than its contemporary snapshot (nuDNA). Our analysis led us to suspect fragmentation in its eastern fork, an area most impacted by human development. We conclude that the boundaries of drainages affect the White Mountains population structure but short, cryptic, overland paths among them likely play a role in replenishing genetic diversity. We also report an extension to the species longevity from 2 to 4 years from genetic recaptures during our six-year study period.

opennotspecifiedSep 2021View details →

Fig. 1 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

Fig. 1. Geographical sampling maps for (A) Apatania and (B) Limnephilus.