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FIGURE 9 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)

FIGURE 9. Austinixa roblesi sp. nov.; A–D, ovigerous female paratype, cw 9.8 mm (USNM 1558340); E, ovigerous female paratype, cw 9.4 mm (ULLZ 12115); F, female paratype, cw 6.6 mm (ULLZ 13143); all from Dangriga, Belize. A, carapace, dorsal; B, enlarged right side of carapace, dorsal; C, carapace frontal region, from anterior; D, right chela, internal; E, left chela, dorsal, F, female pleon. Scale bars = 1.5 mm (A), 1.0 mm (B–F).

FIGURE 5 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)

FIGURE 5. Austinixa artankeri sp. nov.; A, male paratype, cw 7.3 mm (UF 18916); B, male paratype, cw 8.5 mm (ULLZ 13732); C, D, male paratype, cw 6.2 mm (ULLZ 13731); E, ovigerous female paratype, cw 8.5 mm (UF 18928); F, female paratype, cw 8.8 mm (UF 18950); G, ovigerous female paratype, cw 9.0 mm (USNM 1558331); H, ovigerous female paratype, cw 5.8 mm (ULLZ 13644), all from Bocas del Toro, Caribbean coast of Panama. A, right chela, internal, setae not shown; B, male pleon; C, D, left first gonopod, pleonal surface, entire and enlarged tip; E, right chela, internal, setae not shown; left chela, internal, setae not shown. Scale bars = 1.0 mm (A, B, E–H), 0.5 mm (C), 0.25 mm (D).

FIGURE 3 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)

FIGURE 3. Distribution of the species of Austinixa Heard & Manning, 1997. In most cases, latitudinal ranges are shown. For A. cristata, the latitudinal range shown corresponds to the distribution on the Atlantic coast only. Specific locations are shown for records of A. cristata in the Gulf of Mexico, as well as for A. bragantina and three undescribed species (symbols as shown in legend). Only A. bragantina and A. leptodactyla were not included in the present phylogenetic analyses.

FIGURE 2 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)

FIGURE 2. Phylogeny of Pinnotheroidea, with emphasis on Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of concatenated 1415 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 complex (705 bp), the mitochondrial 12S rRNA gene (293 bp) and nuclear histone 3 subunit (328 bp). Maximum Likelihood (ML) bootstrap, Bayesian (BAY) posterior probabilities and maximum parsimony (MP) bootstrap values are shown, in order ML/BAY/MP. "–" indicates a value lower than 50%. When all three values are the same, only one number is shown. If values are lower than 50% for all three, no number is shown. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations). Modified from Palacios Theil et al. (2016) and generic assignments of some species of Pinnixa updated according to Palacios Theil & Felder (2020)

FIGURE 1 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)

FIGURE 1. Consensus tree for Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of 821 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 gene complex. Bootstrap values higher than 50% indicated at internal nodes. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations).

opencc-zeroAug 2020View details →

Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers

Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.

opencc-zeroOct 2020View details →

Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1053 P. americana and other Periplaneta species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the USA.

opencc-zeroDec 2013View details →

Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test if the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of post-glacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian Computation approach but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonisation abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.

opencc-zeroDec 2015View details →

Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.

opencc-zeroDec 2015View details →

Data from: Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers

Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes.

opencc-zeroDec 2010View details →

Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.

opencc-zeroDec 2017View details →

Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.

opencc-zeroDec 2012View details →

Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3′-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3′-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3′-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.

opencc-zeroDec 2013View details →

Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads

Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases the matching Genbank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.

opencc-zeroDec 2013View details →

Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae.

FIGURE 4 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper

FIGURE 4. Species tree of the Vipera ursinii–renardi complex (with V. berus as outgroup) as inferred in *BEAST based on two mitochondrial and three nuclear loci (A); species-tree cloudogram of the complex based on 27 000 post-burn-in trees resulting from 3 runs of *BEAST, each producing 10,000 trees from which 10% was discarded as burn-in. Higher colour densities represent higher levels of certainty. Maximum clade credibility tree is superimposed upon the cloudogram in bold violet (B). Values of posterior probabilities are given. This figure is published in colour in the online version, the colours of the branches correspond with the colour of mitochondrial lineages in Fig. 2A.

FIGURE 1 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper

FIGURE 1. Sampled localities inside the approximate distribution area of Vipera ursinii–renardi complex in Europe. Circles indicate sampling localities of Vipera ursinii–renardi complex, and triangles show the sampling of outgroup taxa. A diamond indicates the type locality of Vipera graeca stat. nov. This figure is published in colour in the online version, the colour of the patches corresponds to the colour of mitochondrial lineages in Fig. 2A.

FIGURE 2 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper

FIGURE 2. (A) Current mitochondrial Bayesian phylogenetic hypothesis of Vipera ursinii–renardi complex based on CYT B dataset of Ferchaud et al. (2012) and Zinenko et al. (2015); (B) Phylogenetic reconstruction of the concatenated dataset (mtDNA+nDNA genes) obtained in MrBayes/Maximum likelihood (see Table 1). Sequences of Vipera berus (Vbbe-HU, Vbbo-AL, Vbni-RO) included as outgroup are not shown. Bayesian posterior probabilities/bootstrap pseudoreplicates are shown at nodes; (C) SplitsTree phylogenetic network (Huson & Bryant 2006) of the dataset for five mitochondrial and nuclear loci sequenced in the present study using the neighbornet algorithm. Asterisks in Fig. 2C indicate both phased sequences in one branch. Numbers along the edges are the bootstrap support values from 1000 replicates. The scale bar indicates one substitution per one hundred nucleotide positions. Taxon names of the phylogenetic network correspond with the Table 1. Inset shows a male Greek Meadow Viper from Dhëmbel Mountains, Albania.

FIGURE 3 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper

FIGURE 3. Nuclear allele networks of the three analysed nuclear loci. Circle sizes are proportional to the number of samples/ sequences, small black circles indicate hypothetical haplotypes (alleles). This figure is published in colour in the online version, the colour of the circles in the network corresponds to the colour of mitochondrial lineages in Fig. 2A.