identifier	taxonID	type	CVterm	format	language	title	description	additionalInformationURL	UsageTerms	rights	Owner	contributor	creator	bibliographicCitation
0398B824FFE7FFBBFD46F945FBB7FDDC.text	0398B824FFE7FFBBFD46F945FBB7FDDC.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Andricus lignicola (Hartig 1840)	<div><p>3.1. Genetic variation in Andricus lignicola populations Amplification results of 117 individuals yielded 18 haplotypes with no indels, nonsense mutations, or stop codons. In the sequences of 433 bp of cyt b gene segment, 375 sites were constant and 58 characters were variable. Of the total variable sites, 21 characters were parsimony uninformative and 37 characters were parsimony informative. Nucleotide frequencies in the haplotypes were 34%, 11%, 9%, and 44% for A, C, G, and T, respectively. There were multiple hits at eight sites (127, 142, 146, 272, 304, 376, 415, and 421). Among other variable sites, there were 30 transitions and 20 transversions (ti/tv = 1.5). T h e protein coding region contained 16 amino acid replacements without any indels or nonsense mutations in the translated protein sequences.</p> <p>When haplotypes and their frequencies were examined we found that the most abundant haplotype was H1, which was detected in 36 individuals representing 8 populations (Table 2). Three haplotypes (H4, H5, and H6) were found as private haplotypes. Interestingly, the Çanakkale population had two of the private haplotypes (H5 and H6). When the populations were examined with respect to their haplotype number the Kütahya population had the highest number of haplotypes (n = 4) followed by Çanakkale, Kahramanmaraş, Uşak, and Kayseri (n = 3). The Balıkesir, İstanbul, Konya, and Manisa populations each had two distinct haplotypes. The remaining populations (Afyon, Antalya, Denizli, Düzce, Eskişehir, and Kırıkkale) had a single type of haplotype in each population. In our study, haplotype richness was uncorrelated with the sampling effort (Spearman correlation: r S = 0.161, n = 117, P = 0.56). Rarefaction analysis results showed that the Chao- 1 estimator would not be calculated for 10 populations, in which there were no doubleton haplotypes (S* 1 = –1). However, Kütahya (S* 1 = 4.5 ± 1.12), Uşak (S* 1 = 3.0 ± 0.01), Kayseri (S* 1 = 3.0 ± 0.01), Balıkesir (S* 1 = 2.5 ± 1.12), and İstanbul (S* 1 = 2.0 ± 0.01) displayed a range of Choa-1 estimator values.</p> <p>The genetic diversity estimates of A. lignicola populations showed that haplotype diversity varied from 0.00 to 0.777 with an average of 0.32519 (Table 3). The highest haplotype diversity (h = 0.7778) was detected in the Kütahya population, followed by the Uşak (h = 0.6889) and Kayseri, Balıkesir, and İstanbul populations (h = 0.6667). Six of the remaining populations showed no haplotype diversity due to the occurrence of only a single type of population, N h</p> <p>: number of haplotypes, h: haplotype diversity, π: nucleotide diversity. haplotype in these populations. Nucleotide diversity ranged between 0.00 and 0.042494. The average nucleotide diversity was calculated as π = 0.0087955 (0.8%). The Uşak population displayed the highest nucleotide diversity estimate (π = 0.042494) followed by the Konya population (π = 0.039415). The mismatch distribution, including all samples, indicated a bimodal profile. The Harpending raggedness index was low (r = 0.0044) but not significant. Overall, Tajima’s D neutrality test (Tajima’s D = 0.47873, P&gt; 0.10) and Fu and Li tests (D * = 0.41064, P&gt; 0.10; F * = 0.50013, P&gt; 0.10) were not significant.</p> <p>A pairwise comparison among A. lignicola haplotypes was conducted to determine the sequence differences. Among all pairwise comparisons, the sequence divergence varied from 0.02% to 10.6% (1 to 46 bp, respectively) (Table 4). The most divergent haplotypes H5 (n = 1, Çanakkale population) and H18 (n = 2, Uşak population) were separated from each other by 46 nucleotides. The least divergence, with 1 bp difference, was determined between H3 (n = 2 Balıkesir) and H4 (n = 1 Balıkesir), H1 (common haplotype) and H8– (n = 2 İstanbul) H16 (n = 4 Kütahya, n = 3 Manisa), H6 (n = 1 Çanakkale) and H7 (n = 8 Çanakkale), H9 (n = 6 Kahramanmaraş, n = 2 Kayseri, n = 1 Kütahya) and H10 (n = 3 Kahramanmaraş)–H11 (n = 5 Kayseri)– H12 (n = 2 Kayseri), H14 (n = 4 Konya, n = 3 Kütahya, n = 5 Uşak), and H17 (n = 3 Uşak) haplotypes.</p> <p>The pairwise F st calculations showed significant genetic differentiation among some populations (Table 5). In particular, two locations showed complete differentiation from some other populations; Antalya was significantly different from Afyon, Denizli, Düzce, Eskişehir, and Kırıkkale (F st = 1); and Kırıkkale was different from Afyon, Antalya, Denizli, Düzce, and Eskişehir (F st = 1). Some of the populations had no genetic differentiation (F st = 0) from each other (Afyon and Denizli, Düzce and Eskişehir populations) because these populations share a single haplotype (H1). Other populations displayed genetic differentiation values on a scale of 0 and 1, with statistically significant support (P &lt;0.001) indicating some degrees of differentiation from each other.</p> <p>3.2. Phylogenetic relationships among Andricus lignicola haplotypes</p> <p>Using PAUP* 4.0b for estimation of phylogenetic relationships among 18 A. lignicola haplotypes, MP and ML produced similar tree topologies with different bootstrap values; thus, only a single phylogenetic tree was shown in Figure 1. MP is a consensus tree of 123 shortest trees, which was produced with CI = 0.691 and 139-step length. For ML analysis, jModeltest was used to determine the mutational model that best approximated the sequence evolution of the data set and calculate the transition and transversion ratios; it identified HKY + I</p> <p>Ak</p> <p>Figure 1. The consensus tree of both MP/ML analyses for the cyt b gene region of A.</p> <p>lignicola. Bootstrap values are shown on the branches for both MP and ML, respectively.</p> <p>Outgroup haplotypes: Ac (Andricus caliciformis) and Ak (Andricus kollari).</p> <p>(Hasegawa et al., 1985) as the best fit model to the data set (I = 0.3778). Thus, this substitution model was utilized in ML and BI analysis. ML and MP trees produced two well-supported clades: clade A is composed of a basally located haplotype (H15) from the Konya population and a small polytomous group of three haplotypes (H14, H17, and H18). However, clade B is larger and composed of two further subclades. Evolutionary relationships were not clearly resolved in small subclades; however, in clade B in the large polytomous part, in addition to the presence of a commonly shared haplotype (H1), all other haplotypes are geographically restricted to the western populations. In spite of a monophyletic grouping of two Balıkesir haplotypes (H3 and H4), the relationships of all other haplotypes showed polytomy that could be due to insufficient time elapsed since divergence between lineages or incomplete lineage sorting (Avise, 2000). Some of the haplotypes representing westerly populations such as H14, H17, H18, and H15 (from Konya, Kütahya, and Uşak) seem to be well-separated from other haplotypes.</p> <p>The tree resulting from the Bayesian analysis (BI) is given in Figure 2 with posterior probabilities on the branches. In the Bayesian tree there is polytomy at the basal part, which comprises H16 (from Kütahya and Manisa), H8 (from İstanbul), H1 (shared common haplotype from Afyon, Denizli, Düzce, Eskişehir, İstanbul, Kahramanmaraş, Kütahya, and Manisa), and a large clade that covers the rest of the haplotypes. In the large clade there is also polytomy composed of H13 (KIR) and H7 (CAN), a monophyletic group including H5 and H6 from Çanakkale population, another monophyletic group including H3 and H4 from Balıkesir, and the third lineagemaking polytomy that includes the remaining haplotypes. Within this lineage two haplogroups are observed to be monophyletic. Of these, the first subclade is composed of a small polyphyletic group, which includes H9 (from Kahramanmaraş, Kayseri, and Kütahya), H10 (from Kahramanmaraş), and H11 and H12 (both from Kayseri). Another polytomic group has a basally located haplotype H2 from Antalya and the small polytomic group composed of H14 (Konya, Kütahya, and Uşak) and H15, H16, and H17 (Uşak).</p> <p>The haplotype network analysis shown in Figure 3 produced three main haplogroups with an additional</p> <p>ESK, IST, KAH, KUT, MAN single haplotype (H2 from Antalya) that could not be connected under the 95% connection limit. H2, with the uppermost substitution value, could not be grouped with other haplotypes. In the obtained TCS network haplotypes of the largest cluster seemed to be derived from H1, which was the most common and, geographically, the most widely distributed haplotype. In the large cluster, H6 and H8 did not connect to any haplotypes other than H1. However, H1 was connected to three hypothetical haplotypes that provided a connection to several other haplotypes, such as H5 and H7. In addition to H5, H6, and H7 haplotypes, H4, H3, and H13 are clustered in the large group of haplotypes of the network (Figure 2). The third haplotype cluster, which formed a small grouping with the uppermost substitution value, belonged to H9. Haplotype 9 seemed to be connected to H12, H10, and H11. The last haplogroup contains H14 with the uppermost value, which was connected to two hypothetical haplotypes with three haplotypes (H15, H17, and H18).</p> <p>The same haplotype groupings were also produced by ABGD analysis and generated four groups, including recursive evaluation of group splitting with the initial partition with prior maximal distance P = 1.67e- 03. The ABGD analysis united H1, H3–H8, H13, and H16 as group 1; H2 as group 2; H9 and H1–H12 as group 3; and H14–H15 and H17–H18 as group 4. The genetic distances were d = 0.0062, 0.021, and 0.0036 for the first, third, and fourth groups, respectively. The genetic distance could not be calculated for the second group due to the presence of a single haplotype in this group. The calculated pairwise genetic distances between each of the four detected groups were 0.037 (between groups 1 and 2), 0.0036 (between groups 1 and 3), and 0.0054 (between groups 1 and 4). Likewise, group 4 showed a distance of 0.049 from group 2 and 0.051 from group 3.</p> <p>AMOVA for revealing population structuring was conducted through several trials in groupings of the populations. They were tested for significant clustering and partitioning of the genetic variation at two/three levels; however, only two of the trial schemes are included in Table 6. In the first trial scheme all populations were considered a distinct group, and it was determined that variation was partitioned among groups with 71.43%, and the remaining variation (28.57%) was at the “within population” level. These results were statistically significant (P &lt;0.001) (Table 6a). On the other hand, when all the populations were divided into four groups based on the groupings obtained after ABGD and haplotype network analyses, an even greater level of genetic partitioning value with statistically significant support was detected; 74.12% of variance components were recovered among groups, 16.03% among populations within groups, and 9.86% within population (Table 6b).</p></div> 	https://treatment.plazi.org/id/0398B824FFE7FFBBFD46F945FBB7FDDC	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Mutun, Serap;Received, Hülya Karagözoğlu;Online, Published	Mutun, Serap, Received, Hülya Karagözoğlu, Online, Published (2015): Investigation of genetic variation among Turkish populations of Andricus lignicola using mitochondrial cytochrome b gene sequence data. Turkish Journal of Zoology 39 (5): 721-733, DOI: 10.3906/zoo-1408-60, URL: http://dx.doi.org/10.3906/zoo-1408-60
0398B824FFEDFFB8FD46FD6EFB75F995.text	0398B824FFEDFFB8FD46FD6EFB75F995.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Andricus lignicola (Hartig 1840)	<div><p>4.1. Genetic variation of Andricus lignicola populations The base pair composition in A. lignicola cyt b haplotypes indicates that the collected data are genuine mitochondrial DNA, since anti-G bias is a characteristic of mitochondrial DNA genes (Zhang and Hewitt, 1996). Neither pseudogenes nor heteroplasmy were detected when A. lignicola haplotypes were compared to the corresponding cyt b region of other insect species. In insect mitochondrial protein-coding gene segments, transitions are observed more often than transversions because of poor or deficient mtDNA repair mechanisms and tautomeric base pairing (Brown et al., 1979). In the sequenced region of A. lignicola, the rate of substitution was well within the range of transition and transversion ratios of other insect species (Jermin and Crozier, 1994).</p> <p>freedom).</p> <p>a) One group: all populations are accepted as a distinct group.</p> <p>A total of 18 haplotypes were detected out of the 117 individuals of A. lignicola. Haplotype 1 (H1) is the most common haplotype and is found in 36 individuals representing eight populations (Afyon, Denizli, Düzce, Eskişehir, İstanbul, Kahramanmaraş, Kütahya, and Manisa). The frequency and wide distribution area across populations of H1 may imply that this haplotype is older than other haplotypes detected in this species. Indeed, phylogeographic studies revealed that more common haplotypes might have had a longer time to disperse through the distribution area compared to more geographically restricted haplotypes that may be derived (Crandall and Templeton, 1993). Moreover, sharing haplotypes between/among populations may entail that A. lignicola had a widespread natural distribution in the region, as proposed by the distribution data of the species.</p> <p>In A. lignicola average nucleotide diversity was 0.8%. In other gall wasp species genetic diversity shows wide variation. In A. coriarius nucleotide diversity was 0.5% in Iranian populations and 0.6% in Lebanese populations; however, in Turkey as it was placed in the main clade, nucleotide diversity was 1.5% (Challis et al., 2007). RFLPbased haplotype and nucleotide diversity were 0.4631 and 0.3204 for A. caputmedusae (Mutun, 2010), 0.8089 and 0.115542 for A. lucidus (Mutun, 2011), and 0.45 and 0.054 for A. quercustozae (Dinç and Mutun, 2011). Overall assessment of the findings confirms high genetic diversity in the Anatolian populations of A. lignicola that is higher than in studied European populations of oak gall wasp species, and well within the range of other gall wasp taxa examined so far from Turkey. On the other hand, with respect to haplotype diversity, the Kütahya population had the highest variation followed by the Uşak population (Table 3). Likewise, the highest nucleotide diversity was estimated for the Uşak population, followed by the Konya and Kütahya populations. However, in six populations (Afyon, Antalya, Denizli, Düzce, Eskişehir, and Kırıkkale) both haplotype and nucleotide diversity could not be observed (both values are 0) due to the detection of a single haplotype. Possible explanations for the low variation may be related to insufficient or different sampling sizes among localities. Haplotype richness is thought to be correlated with sampling size (Kalinowski, 2004); however, in our case there was no significant correlation between number of individuals sampled per population. This was further supported by the Chao-1 estimators in which only five populations displayed positive values. Alternately, speciesspecific demographic factors might have influenced these A. lignicola populations. However, observing only a single haplotype with balanced sampling across the distribution range may well be correlated with parasitoid attacks (Hayward and Stone, 2006), which are common in A. lignicola populations and it may be possible that some of the lineages have been swapped out of these localities. Galls of oak gall wasps can be parasitized by inquilines and parasitoids, leading some of the individuals to fail to develop inside the gall (Bailey et al., 2009). Synophrus politus, for example, infects galls of some cynipid species (Washburn and Cornell, 1981). Infected galls are quite similar in coloration pattern and other phenotypic features when compared with the noninfected galls of A. lignicola. Similar effects have been reported for Andricus burgundus gall wasps (Pujade-Villar et al., 2001); however, there is no report for A. lignicola infected by S. politus (except personal observations). In addition to inquiline and parasitoid attacks, there have been several reports of certain alphaproteobacteria, such as Wolbachia spp., and fungi infecting and causing high mortality in gall wasps during the developmental processes of larvae (Rokas et al., 2002). Parasitic attacks may even skew the sex ratio in oak gall wasps (Atkinson et al., 2003).</p> <p>Pairwise comparisons among eighteen A. lignicola haplotypes revealed that the highest number of base differences in mere counting was between haplotype 5 (Çanakkale population) and haplotype 18 (Uşak population) with 46 nucleotide differences. Morphologically indistinguishable species, or cryptic species, may lie within taxonomically defined species. One way to detect cryptic species is to use DNA barcoding; a higher level of sequence difference (barcoding gap) is observed between species and a lower level of genetic distance is observed within species (Leasi and Norenburg, 2014). Cryptic species may be more common than was once thought (Williams et al., 2012); a new cryptic oak gall wasp species from Turkey and Iran has been described recently that was previously classified under A. coriarius (Challis et al., 2007). The presence of a high sequence difference in our case may imply a cryptic species complex. Our preliminary ABGD analysis provided supporting results with an emphasis on the presence of four hidden lineages within A. lignicola. Since speciation is not always accompanied by morphological changes—in our case both gall wasp characters and overall gall characteristics do not show distinguishable differences—large genetic distances within this traditionally recognized species might be handled carefully and more deeply. Therefore, further research is necessary to identify the presence of a cryptic species complex within A. lignicola. Our largerscale studies to test this hypothesis are ongoing.</p> </div>	https://treatment.plazi.org/id/0398B824FFEDFFB8FD46FD6EFB75F995	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Mutun, Serap;Received, Hülya Karagözoğlu;Online, Published	Mutun, Serap, Received, Hülya Karagözoğlu, Online, Published (2015): Investigation of genetic variation among Turkish populations of Andricus lignicola using mitochondrial cytochrome b gene sequence data. Turkish Journal of Zoology 39 (5): 721-733, DOI: 10.3906/zoo-1408-60, URL: http://dx.doi.org/10.3906/zoo-1408-60
