Haplotype Distribution Pattern Research Articles

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

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings which point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

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

Abstract Climatic oscillation often have influenced the present distribution and intraspecific genetic diversity Oecophylla smaragdina through its wide range of geographical distribution. Previous phylogeographic study of Asian weaver ant population denotes the evidence of distribution of Indian types in Indian, Sri Lanka and SE Asian types in South Asian countries including Bangladesh. However, recent phylogenetic analysis reveals the overlapping distribution of the Indian and South East Asian clades of O. smaragdina in Bangladesh. The present study aims to identify the haplotypes and it’s networking in Bangladesh based on extensive materials. Sampling was executed according to zonation of 5 areas, demarcated by 3 main rivers during the years 2013 to 2018. Adult O. smaragadina workers were collected from 71 colonies of 67 localities belonging to 47 districts of Bangladesh. A total of 25 haplotypes were identified in Bangladesh comprises 13 and 12 of Indian and SE Asian types, respectively from 93 sequences of Cytochrome c oxidase subunit I (COI) gene of 639 bp. The geographical distribution of this haplotype reveals that the Indian haplotypes are mostly located at the western part of Bangladesh while SE Asian haplotypes were dominated in the Eastern part of the country. Central part of Bangladesh has overlapped with the mixture of both Indian and SE Asian haplotypes. The results of the haplotype network give the evidence of recent expansion of O. smaragdina population in Bangladesh and clarify the evidence of presence of many missing haplotypes in refugee.

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.

Phylogeography of the Siberian weasel (Mustela sibirica), based on a mitochondrial DNA analysis

AbstractWe investigated the genetic diversity and distribution pattern of mitochondrial DNA control-region haplotypes across the distributional range of the Siberian weasel (Mustela sibirica) in Eastern Eurasia. We identified 23 haplotypes from 65 individuals sampled from 21 localities. Our analyses showed two major phylogeographical groups: group I comprised continental Russia, Tsushima and Korea, and group II comprised China, Taiwan and Korea. Two novel haplotypes found in the Amur area and one from Gansu Province were closely related to the Tsushima and Taiwan clades, respectively. Phylogeographical and demographic analyses indicated a recent population expansion for group I, whereas no clear evidence for expansion was obtained for group II. The recent expansion of group I is also supported by historical records. Closely related haplotypes were found between the continental populations and the insular populations on Tsushima and Taiwan, suggesting that the ancestors of the insular populations immigrated from the continent via land bridges. The two groups could have evolved allopatrically in parts of eastern Asia differing in climate and vegetation.

Designation of flyways and genetic structure of Woodpigeon Columba palumbus in Europe and Morocco

The Woodpigeon Columba palumbus is an abundant and widespread Palearctic species that uses multiple flyways in Europe. The designation of the main flyways of Woodpigeon in Europe and the study of the genetic structure of the populations are necessary for the sustainable management of this species. Both ringing recovery data of Woodpigeons and mtDNA D-loop sequences from 606 individuals sampled across Europe and in Morocco were used in this study. In total, 763 direct recoveries of birds ringed during the breeding season in 1908–2016 were analysed, while D-loop sequences were analysed from 416 birds sampled in 2014–2018 and 190 individuals that had been sampled in 2004–2009 for a preliminary investigation. In the median-joining network of D-loop haplotypes, six haplogroups were identified in Woodpigeons from various biogeographical populations. Certain differences in the frequency of haplogroups were found between resident Woodpigeons of the Iberian Peninsula and migratory birds from Eastern and Northern Europe. Relatively low genetic variability within the D-loop was observed in samples of resident birds from the Balearic Islands and the Iberian Peninsula. No genetic variation was found in resident Woodpigeons breeding in Morocco. The analysis of ringing recovery data and distribution patterns of different haplotypes confirmed that Woodpigeons from the north and east of Europe use the Eastern Atlantic flyway, while birds breeding in Hungary use the Mediterranean flyway. It is likely that Woodpigeons from south-eastern Russia, eastern Ukraine and birds breeding further east use the Black Sea flyway. It was also confirmed that the majority of Woodpigeons breeding in Belgium are resident or short-distance migrants. Due to the variability identified in the genetic make-up of different populations of Woodpigeons in Europe, we remark the management implications regarding the species that are relevant in various regions of the continent.

Genetic diversity of Bm86 sequences in Rhipicephalus (Boophilus) microplus ticks from Mexico: analysis of haplotype distribution patterns

BackgroundTicks are a problem for cattle production mainly in tropical and subtropical regions, because they generate great economic losses. Acaricides and vaccines have been used to try to keep tick populations under control. This has been proven difficult given the resistance to acaricides and vaccines observed in ticks. Resistance to protein rBm86-based vaccines has been associated with the genetic diversity of Bm86 among the ectoparasite’s populations. So far, neither genetic diversity, nor spatial distribution of circulating Bm86 haplotypes, have been studied within the Mexican territory. Here, we explored the genetic diversity of 125 Bm86 cDNA gene sequences from R. microplus from 10 endemic areas of Mexico by analyzing haplotype distribution patterns to help in understanding the population genetic structure of Mexican ticks.ResultsOur results showed an average nucleotide identity among the Mexican isolates of 98.3%, ranging from 91.1 to 100%. Divergence between the Mexican and Yeerongpilly (the Bm86 reference vaccine antigen) sequences ranged from 3.1 to 7.4%. Based on the geographic distribution of Bm86 haplotypes in Mexico, our results suggest gene flow occurrence within different regions of the Mexican territory, and even the USA.ConclusionsThe polymorphism of Bm86 found in the populations included in this study, could account for the poor efficacy of the current Bm86 antigen based commercial vaccine in many regions of Mexico. Our data may contribute towards designing new, highly-specific, Bm86 antigen vaccine candidates against R. microplus circulating in Mexico.

Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China

The Pleistocene climatic oscillations had profound effects on the demographic history and genetic diversification of plants in arid north-west China where some glacial refugia have been recognized. The genus Ixiolirion comprises three species, of which two, I. tataricum and I. songaricum (endemic), occur in China. In some locations they are sympatric. We investigated their population structure and population history in response to past climatic change using a sample of 619 individuals in 34 populations with nITS and ptDNA sequences. A significant genetic divergence between the two species was supported by a high level of pairwise genetic differentiation, very low gene flow, and phylogenetic analysis showing that I. songaricum haplotypes were monophyletic, whereas those of I. tataricum were polyphyletic. We found significant differentiation and phylogeographic structure in both species. The split of the two species was dated to the late Miocene (∼7 Ma), but deep divergence occurred in the mid-late Quaternary. A similar haplotype distribution pattern was found in both species: one to two dominant haplotypes across most populations, with unique haplotypes in a few populations or a geographic group. The genetic diversity, haplotype number, and haplotype diversity decreased from the Yili Valley to the central Tianshan and Barluk Mountains. Additionally, ptDNA analysis showed that I. tataricum diversified in the eastern Tianshan and Barluk Mountains, which might be due to physical barriers to long distance seed dispersal such as desert. In conclusion, our results indicated that the Yili Valley was likely a glacial refuge for Ixiolirion in China, with postglacial dispersal from the Yili Valley eastward to the eastern Tianshan Mountains, and northward to the Barluk Mountains. The climatic changes in the Miocene and Pleistocene and geographic barriers are important factors driving species divergence and differentiation of Ixiolirion and other taxa.