High Inter-population Differentiation Research Articles

Defining Evolutionary Conservation Units in the Macedonian Crested Newt, Triturus macedonicus (Amphibia; Salamandridae), in a Biodiversity Hotspot

In this study, we used genetic approaches to assess the conservation status of a protected amphibian species, the Macedonian crested newt, Triturus macedonicus, in Northern Pindos National Park (Epirus, Greece). Mitochondrial DNA sequences and multilocus genotypes of individuals from 38 breeding sites were used to infer their phylogenetic position and to detect and measure genetic variation patterns, population genetic structure, and levels of gene flow. The examined individuals fell within two major clades of the Macedonian crested newt phylogeny, being geographically separated by the Aoos River valley and Vikos Gorge. Both groups constitute separate gene pools, bearing private haplotypes and alleles, and the groups were found to be highly differentiated in both their mitochondrial and microsatellite markers. Thus, they meet all of the criteria needed to be characterized as evolutionary significant units (ESUs) that deserve a separate conservation status. Within each ESU, the particularly high inter-population differentiation and low migration rates imply a lack of connectivity between breeding sites and local isolation in favorable habitats. Our results can inform future programs and actions towards the conservation and management of the Macedonian crested newt in the area.

Genetic diversity of Rhododendron redowskianum Maxim., a rare species of Siberian and Far Eastern rhododendrons, based on plastid and nuclear DNA markers

The genetic diversity of 78 individuals of Rhododendron redowskianum Maxim. from five natural populations of different territories of the Far East – Magadan Region, Sakhalin Region, Primorye Territory and Northeast China was studied. Variability of the species according to five markers of plastid DNA was very low. The only one mutation was detected in one of the markers in a singl individual from Sikhote-Alin population. Analysis of the polymorphism of eight nuclear microsatellites, on the contrary, revealed a high level of diversity in all samples (mean values: Aa = 6.44, Ae = 4.43, Ho = 0.514, He = 0.523) and high interpopulation differentiation (FST = 0.299, p < 0.001). Population structure analysis identified four genetic clusters that correspond to the four geographic areas represented. Relationship analysis based on plastid DNA data revealed the ancestral position of R. redowskianum in relation to the closely related species R. camtschaticum Pall. s.l.

American oil palm from Brazil: Genetic diversity, population structure, and core collection

AbstractThe American oil palm [Elaeis oleifera (Knuth) Cortés] has pronounced importance in oil palm breeding programs. Here, a germplasm bank (GB) of E. oleifera plants collected in the Amazon rainforest in Brazil was submitted to single nucleotide polymorphism (SNP) marker identification, selection, and use, aiming to characterize genetic diversity and population structure and to design a core collection (CC). Five hundred and fifty‐three plants from 206 subsamples, collected at 19 localities spread throughout six geographic regions, were submitted to genotyping‐by‐sequencing analysis. A set of 1,827 high‐quality SNP markers was then selected and used to run the genetic diversity and population structure analysis. The genetic diversity found is of moderate degree, and probably only a small portion of the species diversity is represented in the collection. The possible reason for that is the collecting strategy used, which collected subsamples only around the most prominent watercourses in the region. The average degree of genetic differentiation among subsamples is very high, indicating the presence of high interpopulation differentiation. The collection showed a low level of endogamy. The low average gene flow found indicates that genetic isolation caused by drift is occurring, and there is a need to review the conservation strategy. A set of 245 SNPs distributed throughout all 16 chromosomes was used to design CC based on maximizing the strategy of diversity. The optimal adjustment of the validated parameters, maintained while taking fewest subsamples, led to the choice of a model containing 20% of the entire collection as the ideal to form the CC.

Isolation-by-environment as a driver of genetic differentiation among populations of the only broad-leaved evergreen shrub Ammopiptanthus mongolicus in Asian temperate deserts

Whether the effect of migration-selection-drift equilibrium on population structure is governed by spatial or environmental differences is usually elucidated by isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-resistance (IBR) tests. The population structure of Ammopiptanthus mongolicus, a broad-leaved evergreen psammophyte in eastern Central Asia, was previously thought to follow an isolation by distance pattern. However, recent studies have emphasized the effects of environmental factors on its growth and distribution, suggesting an important influence of local adaptation on the genetic structure of the species. Using inter-simple sequence repeat (ISSR) markers, we verified the previously inferred low intra-population variation and high inter-population differentiation. However, in contrast to previous studies, the results of partial Mantel tests and a maximum likelihood population effects mixed model (MLPE) suggested that local climate differences, rather than geographic distances or resistance distances, are the main factor affecting population differentiation. Further analysis with removal of multicollinear climatic variables and univariate MLPE found that summer and winter precipitation were crucial for shaping the current population genetic structure. Since local precipitation is related to the regeneration, colonization, and overwintering survival of A. mongolicus, its influence on demographic change may explain its effect on the population genetic structure. In addition, precipitation is related to terrain despite westward decreases, which explains the independence of genetic difference and geographic distance. The identified role of IBE suggests that collecting germplasm resources from genetically differentiated populations could be a more effective strategy to preserve the overall genetic diversity of the species than the establishment of corridors to enhance gene flow among populations.

Frequency and variability of five non metric dental crown traits in the permanent maxillary dentitions of a racially mixed population from Bengaluru, Karnataka.

Introduction:Evaluation of Tooth Crown non metric traits benefits to assess the biological distance between populations. It is well known that these traits are characterised by a high inter-population differentiation, low sexual dimorphism, and their recording is loaded by relatively small intra and inter observer error. The dental morphological traits are successfully used in the description and explanation of the microevolutionary and ethnogenetic processes. This paper presents the results of the permanent maxillary dentition tooth crown traits differentiation of human populations from Bengaluru.Materials and Methods:The comparative analysis was carried out on the basis of 4 groups for 5 Tooth Crown non metric traits in maxillary permanent dentition using Arizona State University Dental Anthropology System for morphological scoring system of each trait and each score was charted on Osteoware Dental Morphology software.Results:Study analysed 400 dental casts from 4 different ethnic groups. Traits Winging, shovelling, lingual tubercle showed highest expression in Iranians while Cusp of Carabelli's trait expression showed 87% of prevalence in the surveyed group but the Hypocone trait showed the highest expression in Muslims.Conclusion:Traits of the human dentition can be a valuable diagnostic tool for anthropological studies in classifying and characterizing different ethnic groups. According to the results obtained from this study, it can be said that the groups Hindus, Muslims and Christians (Indians) belong to Sundonts, while Iranians fall under sinodonts population group.

Brown trout (Salmo trutta L.) high genetic diversity around the Tyrrhenian Sea as revealed by nuclear and mitochondrial markers

The brown trout (Salmo trutta L.) is widely distributed all around Europe but its natural diversity is threatened by massive stocking with Atlantic domestic strains. Describing the remaining natural genetic diversity and the proportion of domestic hatchery strains in rivers is a prerequisite for smart conservation. The high genetic diversity of brown trout populations around the Tyrrhenian Sea is well known. Use of twelve microsatellites has allowed description of the natural genetic structure of populations and detection of the consequences of stocking. Mitochondrial DNA control region sequences and the LDH-C1* gene enabled placement of each population into one of the six mitochondrial and two allozymic known evolutionary lineages. The Corsican populations showed low intra-population genetic diversity but an exceptionally high level of inter-population differentiation. More southern Tyrrhenian regions exhibited opposite pattern of diversity, partly due to the Atlantic domestic introgression. Globally, the natural structure outlines two north–south clines: high inter-population differentiation and predominance of the Adriatic lineage in the north, but lower inter-population differentiation and the presence of the natural Atlantic lineage in the south. In addition, the Tyrrhenian region is the contact zone between the widespread Adriatic lineage and a local natural Atlantic lineage probably coming from North Africa through the Strait of Gibraltar.

Polymorphism of Chloroplast DNA and Phylogeography of Green Alder (Alnus alnobetula (Ehrh.) K. Koch s. l.) in Asiatic Russia

This paper studies the phylogeography of Alnus alnobetula s. l. in the Asian part of the Russian range with the use of chloroplast DNA (cpDNA) sequences (intergenic spacers trnH-psbA, trnS-trnG, and psaA-trnS). Nine haplotypes were identified as a result of a combination of polymorphism of all sites in 241 plants in 20 populations of A. alnobetula. High interpopulation differentiation (GST = 0.914, NST = 0.928) and a significant phylogeographic structure (NST > GST, p < 0.05) were found. Reconstruction of genealogical relationships of green alder haplotypes revealed five highly divergent genetic lineages: one geographically widespread throughout Siberia and the Urals and several allopatric lines in the Far East of Russia, namely, the Chukotka Peninsula and the mouth of the Yana River, Magadan oblast, Primorye and the central part of Sakhalin Island, and the southern part of Sakhalin Island. Our data confirm that in the past the range of this species in the Far East was fragmented in several refugia that were isolated for a long time in various ice-free regions. This could have contributed to a high level of intraspecific polymorphism of green alder as a result of the divergence of endemic haplotypes, with almost non-overlapping distribution. However, the level of their molecular divergence does not correspond to the level of morphological differences.

Specific features of microsatellite polymorphism in two species of Arabidopsis

The results of an analysis of microsatellite polymorphism in two closely related Arabidopsis species that differing by their crossing types are presented. Considerable genetic diversity was revealed in Arabidopsis thaliana populations located at the northern periphery of the species range (Karelia), which was not typical of self-pollinating species. Populations from the northern boundary of the species range in the basin of Lake Onega were found to be more polymorphic (P99% = 0.43; Hexp = 0.17) as compared to populations of the islands of Lake Ladoga, which are located approximately 300 km to the south (P99% = 0.39; Hexp = 0.15). It is suggested that the high population polymorphism of A. thaliana in the northern part of its range is most likely associated with hostile growing conditions and is the basis for the adaptation processes. A. thaliana populations are highly differentiated (G(ST) = 0.783), which is typical of inbred species. However, such a high interpopulation differentiation is probably due to the low level of gene flow. Specifically, five populations out of seven examined are located on the islands, i.e., are to some extent isolated. These great differences between A. thaliana populations in terms of polymorphism, as well as the high haplotype diversity, suggests postglacial colonization of the Karelian territory by many different ancestral forms. The participation of unique alleles of microsatellite loci with many dinucleotide repeats in the adaptive evolution of A. thaliana is discussed. A species population that is rare for Karelia, Arabidopsis lyrata ssp. petraea, is in complete isolation and, due to specific features of the microevolutionary processes in such populations, is characterized by the polymorphism level, which is low for outbred species (P99% = 0.64; Hexp = 0.16). Nevertheless, this population exists in Karelia for a long period of time, pointing to its successful adaptation to these conditions.

Diachronic Evidence in Nonmetric Morphological Characters of Teeth in Armenian Highland and Georgia Populations

The aim of the study is the assessment of biological distance between populations from Arme-nian highland and Georgia based on the frequency of nonmetric odontological traits. These traits are characterized by high inter-population differentiation, low sexual dimorphism, and relatively small intra and inter observer recordation error. This paper presents the results of the odontological differentiation of human populations from Armenian highland and Georgia. The comparative analysis was carried out on 12 populations. Trait frequencies for all populations were analysed using principal component analysis. Results support the following conclusions: The populations of Armenian highland and Georgia can be differentiated as far as the frequency of odontological traits are concerned. Biocultural diversity of ancient Transcaucasian populations has not been studied extensively, therefore delineating some of the patterns of phenotypic variation may be useful for understanding their ongoing evolution.

A dental non-metric analysis of the Classical/Late Antiquity period (1st century BC–3rd century AD) population from Armenian Plateau

The aim of the study is to assess of the biological distance between the populations from the Armenian Plateau and Georgia, with samples from Eastern Europe, and Central Asia on the basis of the frequency of dental non-metric traits. It is well known that these traits are characterised by high inter-population differentiation, low sexual dimorphism, and their recording is loaded by relatively small intra and inter observer error. The dental non-metric traits are successfully used in the description and explanation of the ethnogenetic processes. The comparative analysis was carried out on the basis of 19 populations. The frequency of the dental non-metric traits among all the populations was analysed using the multiple correspondence analysis and the cluster analysis. Analysis results do not allow to concretize the sources of components of the odontological structure of the Classical/Late Antiquity period populations of the Armenian Highland reducing them to the direct influence of representatives of any cultures or communities. Future dental morphology investigation in Armenia should focus on characterizing, with the aid of an identified skeletal collection, the frequencies of traits on an Armenia large sample. This would be only a gateway to a wider (geographically and, more important, chronologically) dental morphology characterization of Armenian peoples.

Non-Metric Dental Traits in Human Skeletal Remains from Transcaucasian Populations: Phylogenetic and Diachronic Evidence

The aim of the study is the assessment of biological distance between populations from Transcaucasia on the basis of the frequency of dental morphological traits. It is well known that these traits are characterised by a high inter-population differentiation, low sexual dimorphism, and their recording is loaded by relatively small intra and inter observer error. The dental morphological traits are successfully used in the description and explanation of the microevolutionary and ethnogenetic processes. This paper presents the results of the odontological differentiation of human populations from Transcaucasia. The comparative analysis was carried out on the basis of 12 groups. From the obtained results, we can draw the following conclusions: The populations of Armenian Highland and Georgia can be differentiated as far as the frequency of dental morphological traits are concerned. They also do not exhibit similar intragroup variability. Biocultural diversity of ancient Transcaucasian populations has not been studied extensively; therefore, delineating some of the patterns of phenotypic variation may be useful for understanding their ongoing evolution.

Non-metric dental analysis of a Bronze Age population from the Armenian Plateau

The aim of this study is to assess the biological distance between populations from the Armenian highland, Georgia, Eastern Europe, Central Asia and Siberia on the basis of the frequency of non-metric dental traits. It is well known that these traits are characterized by high inter-population differentiation, low sexual dimorphism, and their recording is affected by relatively small intra and inter-observer error.&#x0D; These traits are successfully used in the description and explanation of ethno-genetic processes. Comparative analysis was performed on 30 populations, and the frequency of non-metric dental traits in all populations was determined by principal component analysis. Based on our bio-distance results, we suggest there was a degree of genetic proximity among inland populations of the Armenian Plateau and Transcaucasian area at the beginning of the Bronze Age. The Armenian Plateau and Georgian samples and all those from Kalmykia (Pit Grave culture), the Ukraine (Tripolye culture), the Urals (Sintashtinskaya, Timber Grave cultures), the Volga region (Pit Grave, Balanovo, Fatianovo, Potapovsky cultures) and Central Asia (Gonur-Depe) exhibited close affinities. This conclusion is consistent with that reported by other bio-distance studies examining non-metric cranial traits and Armenian Plateau samples.

Nuclear and chloroplast DNA phylogeography of Ficus hirta: obligate pollination mutualism and constraints on range expansion in response to climate change

This study uses a phylogeographic approach to investigate how interspecific interactions in an obligate pollination mutualism enhance or constrain dispersal and the range distributions of species through time. Fifteen populations of Ficus hirta, a bird-dispersed fig pollinated by a species-specific fig wasp, were sampled from Thailand to the northern limits of the tropical forest in China. These populations were assayed for six nuclear microsatellite loci and two intergenic chloroplast DNA sequences. Analyses of range expansion and genetic clustering indicated a relatively slow rate of range expansion from two or more southern glacial refugia. Low nuclear differentiation, combined with high interpopulation differentiation, and phylogeographic structuring of chloroplast variation indicated that seed dispersal has had a greater constraint than obligate interactions with fig wasps on the rate of post-glacial range expansion. This study is the first to investigate the phylogeographic history of a widely distributed southeast Asian tropical plant whose distribution extends to the northern limits of tropical forest habitat in China. It is also the first study of Ficus utilizing molecular data to evaluate whether species-specific pollination is a limitation or an aid to range expansion in response to climate change.

High intra-population genetic variability and inter-population differentiation in a plateau specialized fish, Triplophysa orientalis

Triplophysa orientalis (Herzenstein) is one of the Nemacheilinae (Cypriniformes: Balitoridae) fish species distributed in the Tibetan Plateau area. In order to understand the impact of plateau uplift on population history and the isolation effect of plateau lakes on T. orientalis, we examined its genetic structure and phylogenetic relationships. A total of 98 individuals from five wild populations, three from plateau lakes and two from branch rivers in upper reaches of the Yangtze River, in the eastern peripheral of the Tibetan Plateau were sampled. An 848 base pair fragment from the mitochondrial DNA (mtDNA) control region was sequenced for analyses. Overall, very high intra-population genetic variability was found in all populations except for one lake population (Rannicuo); nucleotide diversity ranged from 0.0025 to 0.0159 and haplotype diversity ranged from 0.641 to 0.879. Furthermore, the genetic distance between river populations (0.0326) was much higher than that among lake populations (Rannicuo and Barencuo 0.0035, Bannicuo and Yibicuo 0.0038, Rannicuo and Yibicuo 0.0049). Additionally, the analysis of molecular variance demonstrated that most of the observed genetic variability occurred among populations, accompanied with significant Fst values except for that between the Yibicuo and Barencuo populations. This evidence suggested a strong population structure of the species and a lack of inter-population connection. Lastly, the rate of migration indicated there were large historic gene flows among lake populations. Demographic analysis also indicated there were bottlenecks or expansions in three lake populations, suggesting a potential isolation effect of plateau lakes on population differentiation. Molecular dating of intra-specific divergence showed the plateau uplift has shaped the genetic structure of T. orientalis.

Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers

Bittersweet (Solanum dulcamara), a European native weed, is widespread across a variety of habitats and often occurs as a coloniser of open, disturbed, ephemeral environments or wetlands, although it is also found in mountain habitats and on forest edges. As recent studies have shown the potential utility of the species in plant breeding programs, we assembled a collection of bittersweet germplasm from natural populations found in Europe. This collection was analysed with conserved DNA-derived polymorphism (CDDP) and intron-targeting (IT) markers to assess genetic diversity found within and among the populations. We found that there is limited genetic variability within the collected S. dulcamara accessions, with a greater proportion of allelic variation distributed among populations and considerably greater population structure at higher regional levels. Although bittersweet is an outcrossing species, its population structure might be affected by its perennial self-compatible nature, reducing genetic diversity within regional populations and enhancing inbreeding leading to high interpopulation or spatial differentiation. We found that populations have been separated by local selection of alleles, resulting in regional differentiation. This has been accompanied by concurrent loss of genetic diversity within populations, although this process has not affected species-level genetic diversity. Germplasm collecting strategies should be aimed at preserving overall genetic diversity in bittersweet nightshade by expanding sampling to southern Europe and to smaller regional geographic levels in northern and central Europe.

Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery

Black-capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (F(ST) = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.

Protein Polymorphism between 2 Picea abies Populations Revealed by 2-Dimensional Gel Electrophoresis and Tandem Mass Spectrometry

In species with high gene flow and consequent low interpopulation differentiation over wide geographic ranges, differential gene expression along ecological gradients often reveals adaptive significance. We investigated potential differences in protein expression between Picea abies ecotypes adapted to contrasting altitude conditions. Protein expression patterns were compared between needles and roots of 2-month-old P. abies seedlings by means of 2-dimensional electrophoresis. Proteins exhibiting differential expression between the 2 ecotypes were analyzed by tandem mass spectrometry. A total of 19 proteins exhibited qualitative or quantitative polymorphism between the 2 populations. These proteins exhibited organ-specific expression, and the level of interpopulation protein polymorphism was organ dependent. Among differentially expressed proteins, we identified proteins involved in photosynthesis, photorespiration, root tracheary element differentiation, and transmitochondrial membrane transport. Our results show that P. abies seedlings from locally adapted ecotypes exhibit consistent differences in protein expression. The expression polymorphism of some of these proteins has potential adaptive significance.

Genetic structure of the alpine newt, Mesotriton alpestris (Salamandridae, Caudata), in the southern limit of its distribution: Implications for conservation

Tissue samples of Mesotriton alpestris veluchiensis were collected from 11 localities in Greece, and the sequences of two mitochondrial genes (cytochrome b and 16S rRNA), as well as frequencies of 18 allozyme loci, were used in order to describe levels and patterns of genetic variation, identify possible evolutionary units, and reveal aspects of their conservation status. Two major lineages, displaying considerable amount of genetic differences, were supported by both analyses. These lineages, which have been geographically separated since the middle Pleistocene, constitute separate Evolutionary Significant Units (ESUs) and correspond to populations from the Greek mainland and Peloponnisos, respectively. The particularly high inter-population differentiation within each region implies long-term isolation in fragmented habitats, while severe bottlenecking is proposed to have resulted in the observed lack of heterozygotes in the majority of populations. Conservational implications are also discussed, particularly in relation to environmental factors and human activities, which seem to have contributed to the genetic impoverishment of the most marginal populations studied.

Patterns of genetic divergence of three Canarian endemicLotus(Fabaceae): implications for the conservation of the endangeredL. kunkelii

We examined data for 11 allozyme loci in 14 populations that represent the distribution of the endangered Lotus kunkelii, the narrowly distributed L. arinagensis (both endemic to Gran Canaria), and the broad-ranging L. lancerottensis (endemic to the easternmost Canary Islands, Fuerteventura and Lanzarote) to explore and construe patterns of genetic variation and use this data to assess the controversial taxonomic status of L. kunkelii relative to L. lancerottensis. While L. kunkelii maintains low levels of variation, presumably as a consequence of prolonged inbreeding due to very low population size and sharp geographic isolation, the other two taxa have much higher indicators of polymorphism than those reported for other oceanic island endemics. Lotus arinagensis has the highest genetic polymorphism and the lowest interpopulation differentiation, presumably because of its considerable antiquity and habitat stability, despite recent fragmentation. The high interpopulation differentiation in L. lancerottensis is attributed to the Atlantic acting as a barrier, reducing gene flow within islands. Evolutionary analysis of the allozyme evidence indicates that L. kunkelii is genetically closer to L. arinagensis than to L. lancerottensis, thereby dispelling the taxonomic uncertainty and supporting L. kunkelii as a distinct species, warranting legal protection in the forthcoming catalog of threatened Canarian species.

Patterns of allozyme variation in relation to population size of the threatened plantMegaleranthis saniculifolia (Ranunculaceae) in Korea

Patterns of variation at 27 allozyme loci were investigated in the endangered endemic plantMegaleranthis saniculifolia. Levels of allozyme variation (A = 1.47,P = 40%,He = 0.088) were also compared with other endemic plant species. Genetic divergence between populations was very high (Gst = 0.271 ), with moderate to high interpopulation differentiation, which probably arose through historical bottlenecks in a landscape of habitat fragmentation and/or human influence. The percentage of polymorphic loci, heterozygosity, and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles in the smaller populations. Individuals in the small and marginal populations (TB, KD, and CJ) showed higher proportions of fixed loci. These ecologically marginal populations were typically more distant from the nearest neighboring population and were more genetically distinct from one another. The genetic structure of the current population ofM. saniculifolia is probably the result of local extinctions of intervening populations. This, in turn, is due to the Pleistocene climatic change and increased habitat destruction. A positive association appears to exist between genetic diversity and population size. Although these small population sizes are more sensitive to stochastic events, securing a certain number of individuals from the three larger populations (SB, JB, and TG) could be accomplished as part of a conservation strategy. In addition, it is important to prioritize populations in different regions in order to limit population declines caused by large-scale environmental catastrophes.