Haplotype Distribution Pattern Research Articles

A Similarity Matrix for Preserving Haplotype Diversity Amongst Parents in Genomic Selection.

In genomic selection, balancing genetic gain with the preservation of genetic diversity is a critical challenge, requiring innovative approaches to parent selection. Traditional methods risk losing valuable genetic diversity by not fully accounting for the complex patterns of haplotype distribution. To address this, we developed a novel haplotype similarity measure that estimates the genetic similarity amongst offspring from parent pairs by analysing segregating marker patterns and the covariance of additive genetic effects between potential parental gametes. This measure is encapsulated in a novel similarity matrix that quantifies parental genetic relationships and their Mendelian sampling variance, facilitating the selection of parents with diverse haplotypes to maintain genetic diversity. Our method was evaluated through simulation studies and empirical data analysis, indicating that the similarity matrix can help preserve haplotype diversity and potentially improve long-term genetic gains compared to traditional selection methods. These results suggest that the similarity matrix could contribute to more efficient and sustainable genomic selection programs, although further research is necessary to fully understand its impact.

Genetic diversity and phylogeography of the circumboreal peatland violets (Viola epipsila‐V. palustris complex, Violaceae) as inferred from non‐coding nuclear and chloroplast DNA regions

AbstractThe Pleistocene glaciation cycles are a major factor shaping plant genetic diversity, speciation and radiations, and current distribution ranges in the Northern Hemisphere. Case studies are important for improving our understanding of postglacial migration patterns in the Northern Hemisphere taxa in general. Here, we studied the circumboreal Viola epipsila‐V. palustris complex, whose taxonomy and patterns of variation are unclear, and phylogeography unknown, using non‐coding nuclear (ISSRs; inter simple sequence repeats) and chloroplast (cpDNA; trnS‐trnG and trnH‐psbA spacers) DNA regions. Our ISSR results separated five groups corresponding to V. epipsila, V. palustris, V. pluviae, V. suecica and hybrids (V. epipsila × V. palustris). These groups were also confirmed by the genome size of selected samples from each group. The ISSR results showed low within‐population genetic variation in V. epipsila, V. palustris, and V. pluviae as compared to V. suecica, which also has the widest distribution. The cpDNA data allowed us to infer postglacial migration routes and historical impact of gene flow between populations. A total of 13 haplotypes were identified across all species, with the largest number (eight) in European‐eastern Asian‐North American V. suecica. Five haplotypes were present in more than one taxon of the group. The low haplotype variation of European V. epipsila and V. palustris results from their status as glacial relicts. The cpDNA and ISSR phylogenies were congruent. The pattern of haplotype variation and distribution in the ranges of studied species indicates postglacial intercontinental migration of V. suecica across Beringia and V. palustris across the Atlantic.

Accumulation of beneficial haplotypes in Huang-Huai-Hai wheat region and its application in molecular breeding

Accumulation of beneficial haplotypes in Huang-Huai-Hai wheat region and its application in molecular breeding

Plastid marker variation reveals immigration history in Scandinavian Syntrichia norvegica and S. ruralis (Pottiaceae, Bryophyta)

ABSTRACT Introduction Based on previous analyses of Syntrichia norvegica and S. ruralis, the idea of panmictic populations in Scandinavia can be rejected, despite the high dispersal capacities of wind-dispersed spores. We tested, using comprehensive European datasets, whether intraspecific phylogeographical structure reflects glacial and post-glacial history. We expected different entities to indicate immigration from known Late Glacial Maximum refugial areas, and habitat differentiation. Methods Using plastid markers (atpB–rbcL and rpl16), we investigated 45 and 190 Scandinavian and 17 and 15 non-Scandinavian specimens of Syntrichia norvegica and S. ruralis, respectively. Key results We revealed four intraspecific entities in Syntrichia norvegica. Two were from the Scandinavian mountains and the Alps, and one from the Scandinavian mountains only. The fourth was widespread across the Scandinavian mountains, the northern lowlands, and the Baltic Sea islands Öland and Gotland. For S. ruralis, we recovered five entities, of which three were from both Scandinavia and the Alps. One of these occurred in strongly calcareous habitats in southern Scandinavia and the Alps and dominated on Öland and Gotland. One entity was widely distributed only in Scandinavia. One was restricted to the border between boreo-nemoral and southern-boreal Scandinavia. Conclusions The plastid haplotype distribution patterns suggest glacial survival of Syntrichia norvegica and S. ruralis in refugia south, east and possibly within ice-covered areas of Scandinavia. We hypothesise that one S. ruralis entity evolved adaptations to strongly calcareous habitats. The dominance or prevalence of specific haplotypes of both species on Öland and Gotland contributes to the unique biodiversity of these islands.

Genetic diversity and haplotype distribution patterns analysis of cytb and RAG2 sequences in Rana hanluica from southern China.

Rana hanluica: an endemic amphibian of China, is found in the hills and mountains south of the Yangtze River. In this comprehensive study, we collected 162 samples from 14 different localities to delve into the genetic diversity of Rana hanluica using mitochondrial Cytb and nuclear RAG2 as genetic markers. Our findings reveal that the Nanling Mountains, specifically regions like Jiuyi Shan, Jinggang Shan, Mang Shan, and Qiyun Shan, are genetic hotspots harboring remarkable diversity. The research results also indicate that there is gene flow among the various populations of the species, and no distinct population structure has formed, which may be due to migration. Moreover, populations in some regions, as well as the overall population, show signs of a possible genetic bottleneck, which we speculate may have been caused by climate change. However, given the exploratory nature of our study, further investigations are warranted to confirm these observations. Through phylogenetic analyses, we uncovered indications that R. hanluica might have originated within the Nanling region, dispersing along the east-west mountain ranges, with a significant contribution originating from Jiuyi Shan. The genetic distributions uncovered through our research reflect historical migratory patterns, evident in the distinct haplotypes of the RAG2 gene between the western and eastern parts of the studied area. Moreover, Heng Shan and Yangming Shan exhibited unique genetic signatures, possibly influenced by geographic isolation, which has shaped their distinct genotypes. The insights gained from this study hold profound implications for conservation efforts. By identifying regions rich in genetic diversity and crucial gene flow corridors, we can develop more effective conservation strategies. Preserving these genetically diverse areas, especially within the Nanling Mountains, is vital for maintaining the evolutionary potential of R. hanluica. In conclusion, our research has laid a solid foundation for understanding the genetic landscape of R. hanluica, shedding light on its origins, population structures, and evolutionary trajectories. This knowledge will undoubtedly guide future research endeavors and inform conservation strategies for this endemic amphibian.

Relict stands of Central European oaks: Unravelling autochthony and genetic structure based on a multi-population study

Relict stands of Central European oaks: Unravelling autochthony and genetic structure based on a multi-population study

Distribution of genetic diversity of neotropical Biomphalaria (Preston 1910) (Basommatophora: Planorbidae) intermediate hosts for schistosomiasis in Southeast Brazil

IntroductionBiomphalaria glabrata, B. tenagophila, and B. straminea occurrence are crucial for estimating the risk of infectious human schistosomiasis in the neotropics. How different geographic sample strategies influence snail genetic diversity estimations were here investigated for three Schistosoma mansoni hosts.MethodsMitochondrial gene sequences were employed for Cytochrome C Oxidase I (COI), ribosomal RNA (rRNA) 16S, and a dataset with concatenated gene sequences (COI+16S), resulting in an improved scientific hypothesis regarding the geographical distribution of snail species. This study compared the sequences of snails from the Middle Paranapanema (MP) hydrographic basin in a geographically restricted area (inner group) to snails widely distributed across a broad geographical range in São Paulo (outer group), Brazil from 1999 to 2017. DNA sequence polymorphisms and haplotype diversity were estimated using DNAsp software. Haplotype network trees were constructed using a network program. The geographical distribution of the haplotypes was mapped using QGIS. Haplotype variation and distribution were tested for population structure using analysis of molecular variance (AMOVA).Results and discussionThe genetic diversity of B. glabrata, sampled from disconnected but geographically close freshwater collections, was partitioned into two sequence groups. The haplotype network showed that the diversity of B. straminea was more spatially partitioned than in B. tenagophila, which exhibited two population groups. The haplotype distribution pattern for B. tenagophila showed many unique and exclusive haplotypes for all three loci. AMOVA showed that genetic diversity could be high in species inhabiting small geographical areas, and a large river is not a local geographical barrier for snail migration. This study found that the survey dimensions and snail samplings influenced the genetic diversity results obtained by mitochondrial DNA molecular markers.

Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China.

Tianshan Mountains provide a model for studying biological evolution and speciation. Here we assess the evolutionary history of Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB), which are sympatric in the Yili River Valley in Xinjiang, China.Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI, COII, Cytb) and four nuclear DNA (nuDNA, EF-1α, Wingless, RPS5, CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan), and MNS (Manasi).Our results reveal that there is an asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggests that the genetic divergence between the two species in this area may have occurred in Holocene at 0.008 Mya. Neutrality tests (Tajima's D, Fu's F s), and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past. The demographic history and gene flow pattern between ACB and ECB may follow the "mountain isolation" hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are grouped together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear for both ACB and ECB, supporting that there has been frequent gene flow among the geographic populations in the Tianshan Mountains.These findings indicate that the Tianshan Mountains are less likely a barrier to gene flow of the two species.

Molecular evidence for natural hybridization between Rumex crispus and R. obtusifolius (Polygonaceae) in Korea

Interspecific hybridization has been suggested to occur frequently in Rumex (Polygonaceae). Several hypothesized combinations of parental species of hybrids based on their intermediate morphology have been suggested in the genus, but few of them have been phylogenetically tested. We analyzed nuclear and chloroplast DNA sequence data of a putative natural hybrid between Rumex crispus and Rumex obtusifolius from Korea to confirm its hybrid status and to determine the maternal parent. Analysis of the nuclear DNA pgiC region revealed that R. crispus and R. obtusifolius have contributed to the nuclear genome of the putative hybrids. The haplotype distribution pattern inferred from the combined sequence data set of five chloroplast DNA regions (matK, rbcL-accD IGS, trnK-rps16 IGS, ycf6-psbM IGS and psbA-trnH IGS) indicated bidirectional hybridization events between R. crispus and R. obtusifolius. This paper provides the first molecular evidence for interspecific hybridization between R. crispus and R. obtusifolius. In addition, our findings strongly suggested that Korean populations of Rumex japonicus have a hybrid origin, and R. crispus may represent one of the parental taxa.

Phylogeography and demographic inference of the endangered sei whale, with implications for conservation

Abstract The sei whale (Balaenoptera borealis) presents a disjointed geographic distribution. Significant genetic divergence between sei whales from the North Atlantic (NA) and North Pacific (NP) have been recorded; however, limited samples from the Southern Hemisphere (SH) have precluded a global analysis. The largest recorded mass mortality event occurred in Golfo de Penas, southern Chile, providing a primary source of SH samples. A global mitochondrial DNA phylogeographic study was undertaken including 111 SH samples (98 from Golfo de Penas), and new sequences from the NP. A marked phylogeographic structure was observed between the three ocean basins' populations, with the highest ΦST values between NA–NP and NA–SH, and a lower but still significant value between SH–NP. This structure, and the haplotype distribution pattern, suggest a more recent separation between SH–NP and an absence of recurrent gene flow among all three populations. Only one potential migratory event was detected from SH to NA. These results support an ongoing phylogeographic differentiation between all populations, highlighting the identity of each and the importance of independent management. Therefore, each population should represent a separate management unit, which is important in the development of conservation strategies. Demographic analyses detected a recent reduction of population size in the SH and NA, but not in the NP. For all populations, estimated effective population sizes were higher than estimated census sizes. This suggests that most of the genetic diversity of pre‐whaling populations is still retained; however, continued reduction in population sizes could lead to future loss of genetic diversity. This study highlights the necessity of local protection and systematic monitoring of the Golfo de Penas sei whale population. In such a remote area the use of remote sensing techniques could be a cost‐effective option for evaluating the threat, periodicity and magnitude of mortalities and their effect on the local whale population. The integration of genetic and demographic approaches improves the understanding of the dynamics of populations, which is particularly useful in endangered species.

Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex

BackgroundPlant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes.ResultsThe ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM).ConclusionsPliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.

Genetic analysis and population genetic structure of hard-shelled mussel, Mytilus coruscus Gould 1861 (Mytiloida: Mytilidae) from the coasts of South Korea based on mitochondrial cytochrome oxidase (COI) gene sequences.

Mytilus coruscus Gould, 1861 is a mussel species in the family Mytilidae, native to the Northwest Pacific Ocean, ranging from the East China Sea, the Yellow Sea, and as far as the Peter the Great Gulf in the East Sea. In Korea, this species has been heavily exploited for nutrient-rich food resources and experienced severe reduction in their population. The aim of this study was to investigate the genetic diversity and population structure and to provide baseline data to facilitate the conservation and sustainable use of the vulnerable species M. coruscus in South Korea. Mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequences of 91 adult individuals from four islands and one coastal localities in South Korea were sequenced. We then compared genetic diversity and haplotype data with previously published Chinese wild populations. Mytilus coruscus populations on Korean coasts were found to exhibit high genetic diversity despite concerns regarding recent population reduction. A total of 42 haplotypes were defined by 56 polymorphic sites. High-level genetic diversity was observed on four Island sites (Hd = 0.906-0.955, π = 0.0068-0.0090). The other seashore site represented relatively lower genetic diversity (Hd = 0.529, π = 0.0011) and was genetically differentiated from the others. In a previous study, wild populations on the East China Sea exhibited similarly high genetic diversity as that observed in our study. Additionally, Chinese M. coruscus populations exhibit a distinct regional haplotype distribution pattern while sharing six haplotypes with Korean populations. The results of this study provide insights that further the current understanding regarding the evolution of M. coruscus species and provides comprehensive genetic data to facilitate the development of an effective conservation strategy.

Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China.

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (HE = 0.160–0.361, with the exception of K. obovata) and high levels of inbreeding (FIS = 0.104–0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [FST = 0.165–0.629 (nSSR); GST = 0.173–0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

Distribution of HLA class Ⅰ and class Ⅱ haplotypes in Chinese Han population based on family segregation

HLA haplotype analysis has important application value in human population genetics, anthropological research and HLA matching transplantation. Based on HLA-A, -B, -C, -DRB1 and -DQB1 genotyping data from 663 families including 663 leukemia patients and 991 related donors, the allele frequency (AF) and haplotype frequency (HF) of two-, three- and five-locus haplotype distribution patterns in the Chinese Han population were determined by family segregation. A total of 38 alleles at A locus, 75 alleles at B locus, 35 alleles at C locus, 53 alleles at DRB1 locus and 22 alleles at DQB1 locus were discovered in this population. The frequencies of these alleles were basically consistent with those of previous reports except for some tiny differences. The study found 11 A-C, 15 C-B, 4 B-DRB1 and 11 DRB1-DQB1 two-locus haplotypes with a frequency over 2%. The number of A-C-B and A-B-DRB1 three-locus haplotype with a frequency over 1% were 11 and 3 respectively. The most common HLA-A-C-B-DRB1-DQB1 haplotype (HF>1%) were A*3001-C*0602-B*1302-DR*0701-DQ*0202 (4.30%), A*0207-C*0102-B*4601-DR*0901-DQ*0303 (3.07%), A*3303-C*0302-B*5801-DR*0301-DQ*0201 (1.49%) and A*1101-C*0102-B*4601-DR*0901-DQ*0303 (1.01%). The results are helpful for finding matching donors for hematopoietic stem cell transplant patients and also contribute to transplant immunology, HLA-related diseases, research of human genetics and other fields.

Haplotype diversity and distribution pattern of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh based on mitochondrial COI genes

Haplotype diversity and distribution pattern of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh based on mitochondrial COI genes

Phylogeography and potential glacial refugia of terrestrial gastropod Faustina faustina (Rossm\xe4ssler, 1835) (Gastropoda: Eupulmonata: Helicidae) inferred from molecular data and species distribution models

Faustina faustina is a conchologically highly diverse forest gastropod with several morphological forms. It is a Carpathian species, but it also occurs in northern isolated localities, where it was probably introduced. We performed the first phylogeographic analysis of 22 populations, based on three molecular markers: COI, ITS-2, and 28S rRNA. Genetic data were complemented by paleo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. We discovered high genetic variability of COI sequences with p-distances between haplotypes ranged from 0.2 to 18.1% (6.3–16.6% between clades). For nuclear markers, a haplotype distribution pattern was revealed. Species distribution models indicated a few potential refugia in the Carpathians, with the most climatically stable and largest areas in the Southern Carpathians. In some climate scenarios, putative microrefugia were also predicted in the Western and Eastern Carpathians, and in the Apuseni Mts. Our results suggest the glacial in situ survival of F. faustina and its Holocene expansion in the Sudetes. Although our genetic data as well as shell phenotypes showed considerable variation within and between studied populations, the molecular species delimitation approaches still imply only one single species. Our study contributes to the understanding of the impact of processes on shaping contemporary population genetic structure and diversity in low-dispersal, forest species.

Analyzing a putative enhancer of optic disc morphology

BackgroundGenome-wide association studies have identified the CDC7-TGFBR3 intergenic region on chromosome 1 to be strongly associated with optic disc area size. The mechanism of its function remained unclear until new data on eQTL markers emerged from the Genotype-Tissue Expression project. The target region was found to contain a strong silencer of the distal (800 kb) Transcription Factor (TF) gene GFI1 (Growth Factor Independent Transcription Repressor 1) specifically in neuroendocrine cells (pituitary gland). GFI1 has also been reported to be involved in the development of sensory neurons and hematopoiesis. Therefore, GFI1, being a developmental gene, is likely to affect optic disc area size by altering the expression of the associated genes via long-range interactions.ResultsDistribution of haplotypes in the putative enhancer region has been assessed using the data on four continental supergroups generated by the 1000 Genomes Project. The East Asian (EAS) populations were shown to manifest a highly homogenous unimodal haplotype distribution pattern within the region with the major haplotype occurring with the frequency of 0.9. Another European specific haplotype was observed with the frequency of 0.21. The major haplotype appears to be involved in silencing GFI1repressor gene expression, which might be the cause of increased optic disc area characteristic of the EAS populations.The enhancer/eQTL region overlaps AluJo element, which implies that this particular regulatory element is primate-specific and confined to few tissues.ConclusionPopulation specific distribution of GFI1 enhancer alleles may predispose certain ethnic groups to glaucoma.

COI-5P Gene Sequence Variation in Philippine Hydropuntia edulis (Gracilariaceae, Rhodophyta)

Hydropuntia edulisis an agar producing seaweed. In part due to its economic relevance, the last few decades have seen substantial efforts toward exploring its uses. With these developments, information on its genetic diversity is still, however, incipient. Here, phylogenetic and haplotype analyses in Philippine H. edulis were performed based on mtDNA COI-5P gene sequences. Using our newly generated dataset and previous accessions, the range of pairwise intra- and interspecific differences in H. edulis was determined. A total of 14 H. edulis haplotypes were recovered, of which seven were newly detected. Ten (10) haplotypes were found in the Philippines, eight of which appeared to be exclusive in the region. The genetic relationships in H. edulis as inferred from phylogenetic and haplotype network analyses did not follow a clear biogeographic structure. Future work will be necessary to explore the lack of detectable haplotype distribution pattern as presently found. This study can be seen as a fundamental point for future research on the management and conservation of H. edulis in the Philippines.

Genetic Diversity and Population Structure of Acanthochiton rubrolineatus (Polyplacophora) Based on Mitochondrial and Nuclear Gene Markers

Acanthochiton rubrolineatus (Cryptoplacidae, Neoloricata, Polyplacophora) has a narrow distribution range along the seacoasts of China, the Korean Peninsula and Japan. We collected 238 samples from eight localities along the Chinese coast, and analyzed the genetic diversity and population structure with COI, 16S-rRNA and 28S-rRNA gene sequences. All analyses based on combined sequences of COI and 16S-rRNA suggested that there was evident genetic differentiation between the northern populations (YT, WH, DL, QD, LYG) and southern populations (ZS, YH, XM) of A. rubrolineatus. The haplotype distribution pattern and genetic diversity based on 28S-rRNA sequences also supported the genetic divergence between the two groups. Both groups had experienced population expansion after the ice age of Pleistocene, and an additional population bottleneck had happened in the southern group in recent history, which led to low genetic diversity of mitochondrial DNA and abnormally high diversity of nuclear DNA in this group. Our results suggested that the protection on A. rubrolineatus is necessary, and the northern and southern group should be protected separately.

Genetic diversity of Tulipa suaveolens (Liliaceae) and its evolutionary relationship with early cultivars of T. gesneriana

Polychromatic Tulipa suaveolens occurs over a vast territory ranging from the Crimea to eastern Kazakhstan. Its phylogenetic relationship to cultivated T. gesneriana is still under discussion. We used sequences from the psbE–petL region of chloroplast DNA and the complete internal transcribed spacer of nuclear ribosomal DNA to examine the genetic variability of T. suaveolens specimens from European Russia and the adjoining regions. Our data set also included 8 varieties of cultivated T. gesneriana. The research on biogeographic patterns of plastid haplotype and nuclear ribotype distribution provides evidence that their origin and dispersal over the Lower and Middle Volga Region are linked to the Khazar or Early Khvalynian transgression of the Caspian Sea and subsequent events. In the Crimea and the adjacent regions, the pattern of haplotypes’ distribution indicates that their origin and expansion may be linked to the Karangat transgression of the Black Sea and the subsequent New Euxinian regression. Based on our results, we propose that T. suaveolens is the likeliest wild ancestor of early T. gesneriana.