Elucidating the multiple genetic lineages and population genetic structure of the brooding coral <Emphasis Type="Italic">Seriatopora</Emphasis> (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F _ST = 0.064–0.116 (all P = 0.001), pairwise G′′_ST = 0.107–0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.     

Unspecific histological and hematological alterations in anadromous and resident <Emphasis Type="Italic">Salvelinus malma</Emphasis> induced by volcanogenic pollution

Knowledge of larval dispersal and connectivity in coral reef species is crucial for understanding population dynamics, resilience, and evolution of species. Here, we use ten microsatellites and one mitochondrial marker (cytochrome b) to investigate the genetic population structure, genetic diversity, and historical demography of the powder-blue tang Acanthurus leucosternon across more than 1000 km of the scarcely studied Eastern African region. The global AMOVA results based on microsatellites reveal a low but significant F _ST value (F _ST = 0.00252 P < 0.001; D _EST = 0.025 P = 0.0018) for the 336 specimens sampled at ten sample sites, while no significant differentiation could be found in the mitochondrial cytochrome b dataset. On the other hand, pairwise F _ST, PCOA, and hierarchical analysis failed to identify any genetic breaks among the Eastern African populations, supporting the hypothesis of genetic homogeneity. The observed genetic homogeneity among Eastern African sample sites can be explained by the lengthy post-larval stage of A. leucosternon, which can potentiate long-distance dispersal. Tests of neutrality and mismatch distribution signal a population expansion during the mid-Pleistocene period.     

Phylogeographical structure inferred from cpDNA sequence variation of <Emphasis Type="Italic">Zygophyllum xanthoxylon</Emphasis> across north-west China

Zygophyllum xanthoxylon, a desert species, displaying a broad east–west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.     

Genetic consequences of anthropogenic disturbances and population fragmentation in <Emphasis Type="Italic">Acacia senegal</Emphasis>

Acacia senegal is endemic to dry forest and woodland ecosystems of Sub-Saharan Africa and provides both ecological and socio-economic benefits. However, these ecosystems are threatened by escalating human disturbances and fragmentation. To investigate the human impacts on genetic diversity and structure of A. senegal, we studied genetic variability and differentiation of 330 individual trees from 11 natural A. senegal populations, grouped into lightly and heavily disturbed, using 12 polymorphic nuclear microsatellite markers. Gene diversity (H _E ) ranged from H _E = 0.570 to H _E = 0.632. Significant differences (P < 0.05) between the levels of disturbances are reported for mean gene diversity, number of alleles and allelic richness with lightly disturbed populations showing higher values. Overall, the indirect estimates of average outcrossing rates ranged from 0.794 (Kiserian) to 0.999 (Kampi ya Moto) with a mean of 0.997 suggesting a predominantly outcrossing species. There was no significant relationship (P > 0.05) detected between genetic and geographic distances, showing lack of isolation by distance. Analysis of population structure using unweighted pair group method with arithmetic mean and Bayesian model suggests presence of three gene pools as most probable, although most individuals showed mixed ancestry. The diversity and genetic structure reported in this study revealed negative impacts of human disturbance on A. senegal within this ecosystem. We recommend in-situ conservation strategies to safeguard the woodland ecosystem from further deforestation.     

Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (<Emphasis Type="Italic">Egretta eulophotes</Emphasis>)

Major histocompatibility complex (MHC) genes are excellent markers for the study of adaptive genetic variation occurring over different geographical scales. The Chinese egret (Egretta eulophotes) is a vulnerable ardeid species with an estimated global population of 2600–3400 individuals. In this study, we sampled 172 individuals of this egret (approximately 6 % of the global population) from five natural populations that span the entire distribution range of this species in China. We examined their population genetic diversity and geographical differentiation at three MHC class II DAB genes by identifying eight exon 2 alleles at Egeu-DAB1, eight at Egeu-DAB2 and four at Egeu-DAB3. Allelic distributions at each of these three Egeu-DAB loci varied substantially within the five populations, while levels of genetic diversity varied slightly among the populations. Analysis of molecular variance showed low but significant genetic differentiation among five populations at all three Egeu-DAB loci (haplotype-based ?_ST: 0.029, 0.020 and 0.042; and distance-based ?_ST: 0.036, 0.027 and 0.043, respectively; all P < 0.01). The Mantel test suggested that this significant population genetic differentiation was likely due to an isolation-by-distance pattern of MHC evolution. However, the phylogenetic analyses and the Bayesian clustering analysis based on the three Egeu-DAB loci indicated that there was little geographical structuring of the genetic differentiation among five populations. These results provide fundamental population information for the conservation genetics of the vulnerable Chinese egret.     

Genetic population structure and low genetic diversity in the over-exploited sea cucumber <Emphasis Type="Italic">Holothuria edulis</Emphasis> Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H _E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H _E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ _ST = 0.49, P < 0.0001; 16S: Φ _ST = 0.34, P < 0.0001; H3: Φ _ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ _ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.     

Comparison of molecular genetic utilities of TD,AFLP, and MSAP among the accessions of <Emphasis Type="Italic">japonica,indica</Emphasis>, and <Emphasis Type="Italic">Tongil</Emphasis> of <Emphasis Type="Italic">Oryza sativa</Emphasis> L.

Rice is one of the most important food crops in the world. Genetic diversity is essential for cultivar improvement programs. We compared genetic diversity derived from insertion–deletion (in–del) or base substitutions by amplified fragment length polymorphism (AFLP), from transposon transposition mutations by transposon display (TD), and from cytosine methylation by methylation-sensitive amplified polymorphism (MSAP) in japonica, indica, and Tongil type varieties of Oryza sativa L. Polymorphic profiles from the three marker systems allowed us to clearly distinguish the three types of varieties. The indica type varieties showed the highest genetic diversity followed by the Tongil and japonica type varieties. Of the three marker systems, TD produced the highest marker indices, and AFLP and MSAP produced similar marker indices. Pair-wise comparisons of the three marker systems showed that the correlation between the two genetic markers systems (AFLP and TD, r = 0.959) was higher than the correlations between the genetic and epigenetic marker systems (AFLP and MSAP, r = 0.52; TD and MSAP, r = 0.505). Both genetic marker systems had similar levels of gene differentiation (G _ST ) and gene flow (N _m ), which differed in the epigenetic marker system. Although the G _ST of the epigenetic marker system was lower than the genetic marker systems, the N _m of the epigenetic marker system was higher than in the genetic marker systems, indicating that epigenetic variations have a greater influence than genetic variations among the O. sativa L. types.     

Integrating genetics and suitability modelling to bolster climate change adaptation planning in Patagonian <Emphasis Type="Italic">Nothofagus</Emphasis> forests

We investigated the impact of past changes in habitat suitability on the current patterns of genetic diversity of two southern beeches (Nothofagus nervosa and Nothofagus obliqua) in their eastern fragmented range in Patagonian Argentina, and model likely future threats to their population genetic structure. Our goal was to develop a spatially-explicit strategy for guiding conservation and management interventions in light of climate change. We combined suitability modelling under current, past (Last Glacial Maximum ~ 21,000 bp), and future (2050s) climatic conditions with genetic characterization data based on chloroplast DNA, isozymes, and microsatellites. We show the complementary usefulness of the distribution of chloroplast haplotypes and locally common allelic richness calculated from microsatellite data for identifying the locations of putative glacial refugia. Our findings suggest that contemporary hotspots of genetic diversity correspond to convergence zones of different expansion routes, most likely as a consequence of admixture processes. Future suitability predictions suggest that climate change might differentially affect both species. All genetically most diverse populations of N. nervosa and several of N. obliqua are located in areas that may be most severely impacted by climate change, calling for forward-looking conservation interventions. We propose a practical spatially- explicit strategy to target conservation interventions distinguishing priority populations for (1) in situ conservation (hotspots of genetic diversity likely to remain suitable under climate change), (2) ex situ conservation in areas where high genetic diversity overlaps with high likelihood of drastic climate change, (3) vulnerable populations (areas expected to be negatively affected by climate change), and (4) potential expansion areas under climate change.     

Phylogeography and historical demography of the orchid bee <Emphasis Type="Italic">Euglossa iopoecila</Emphasis>: signs of vicariant events associated to Quaternary climatic changes

The aim of this study was to investigate whether Pleistocene climatic instability influenced the phylogeographic structure and historical demography of an endemic Atlantic Forest (AF) orchid bee, Euglossa iopoecila Dressler, which shows two main patterns of integument colors over of its geographical distribution. We based our analysis on the concatenated sequence of four mtDNA segments belonging to genes 16S (357 bp), Cytb (651 bp) and COI (1206 bp), totaling 2234 bp. Samples of E. iopoecila populations were collected in 14 AF remnants along its geographic distribution. Median-Joining haplotype networks, SAMOVA and BAPS results indicated three lineages (southern, central and northern clusters) for E. iopoecila, with two important phylogeographic ruptures. We found higher genetic diversity among samples collected in the central region of the AF, which coincides with predicted areas of climatic stability, according to recent AF stability–extinction model. The demographic analysis suggests that only the southern cluster had undergone recent population expansion, which probably started after the last glacial maximum (LGM). Our data suggest that the differentiation observed in the three mitochondrial lineages of E. iopoecila is the result of past disconnections and multiple extinction/recolonization events involving climate fluctuations. In terms of conservation, we would emphasize the importance of considering: (1) the region of the central clade as the location of the highest genetic diversity of mtDNA of E. iopoecila populations; (2) the philopatric behavior of females that tends to restrict mtDNA gene flow in particular, with direct implications for the conservation of the total genetic diversity in euglossine populations.     

Development of microsatellite markers and their use in genetic diversity and population structure analysis in <Emphasis Type="Italic">Casuarina</Emphasis>

Casuarina is a widely cultivated plantation tree species in coastal India, primarily due to its fast growth, high productivity and suitable for pulp and paper production. However, genetic studies of Casuarina have been hindered by lack of genomic resources and genetic markers. Knowledge of the genetic diversity and population structure of Casuarina germplasms will provide the basis for utilizing and improving resource in the breeding program. Keeping this in view, in the present study, we have identified a total of 11,503 simple sequence repeat (SSR) makers from 86,415 expressed sequence tags (ESTs) of Casuarina equisetifolia and C. junghuhniana after redundancy elimination. Dinucleotide repeats were the most abundant accounting for 72.5 % of all microsatellites, followed by trimer (23.4 %), hexamer (1.7 %), tetramer (1.5 %), and very few pentamer (0.6 %) repeats. Of these, 50 markers were used to estimate genetic diversity and population structure among 96 accessions of C. cunninghamiana and C. junghuhniana. EST-SSR markers revealed high level of polymorphism, detecting a total of 829 alleles with an average of 17 alleles per locus. Polymorphic information content (PIC) values ranged from 0.32 to 0.93, with an average of 0.78 per locus. The average observed (H _o ) and expected heterozygosity (H _e ) obtained was high and fairly similar in C. cunninghamiana and C. junghuhniana, thereby suggesting highly heterogeneous nature of Casuarina. Population structure using a Bayesian model-based clustering approach identified clear delineation between C. cunninghamiana and C junghuhniana. Further, these markers were also evaluated in four species of Casuarina confirming high rate of cross-species transferability. The results of this study can provide valuable insights for genetic and genomic research in Casuarina.     

Genetic Differentiation of Colombian Populations of <Emphasis Type="Italic">Anopheles darlingi</Emphasis> Root (Diptera: Culicidae)

Anopheles darlingi Root is a primary vector of malaria in the neotropic region, a species not just highly anthropophilic but very efficient in transmitting Plasmodium species and considered the most important vector in the Amazon region. The main goal of this study was to determine the genetic structure of the A. darlingi populations using microsatellites (STR) in western and eastern regions of Colombia. DNA extraction was done with the cited protocol of band using the Genomic Prep? cell and tissue isolation commercial kits. We used the STR reported by Conn et al (Mol Ecol Notes 1: 223-225, 2001). The analysis with STR proved there was a high genetic diversity and significant alterations of the Hardy-Weinberg equilibrium. The greatest genetic diversity was recorded in Mitu (Vaupes) (Na = 14, Ho = 0.520). The lowest was in Pueblo Nuevo (Cordoba) (Na = 12, Ho = 0.457). The eastern region and the Mitu (Vaupes) populations presented the highest number of primer alleles (Ap = 30; Ap = 13; Ap = 9), with variations between 0.010 and 0.097. The AMOVA revealed that the whole population underwent moderate genetic differentiation (F _ST = 0.063, p < 0.05). The same differentiation was noticed (0.06 < F _ST > 0.06, p < 0.05) with five of the six populations included in this job, and there was a low differentiation in the Las Margaritas (Santander) area (F _ST = 0.02s3, p < 0.05). Our results suggest a slight positive correlation, which does not show a statistical significance between the geographic and genetic distances, probably suggesting that the moderate genetic differentiation found between pairs of populations does not need to be explained for the hypothesis of separation by distance.     

Conservation genetics of the annual hemiparasitic plant <Emphasis Type="Italic">Melampyrum sylvaticum</Emphasis> (Orobanchaceae) in the UK and Scandinavia

Melampyrum sylvaticum is an endangered annual hemiparasitic plant that is found in only 19 small and isolated populations in the United Kingdom (UK). To evaluate the genetic consequences of this patchy distribution we compared levels of diversity, inbreeding and differentiation from ten populations from the UK with eight relatively large populations from Sweden and Norway where the species is more continuously distributed. We demonstrate that in both the UK and Scandinavia, the species is highly inbreeding (global F _IS = 0.899). Levels of population differentiation were high (F’_ST = 0.892) and significantly higher amongst UK populations (F’_ST = 0.949) than Scandinavian populations (F’_ST = 0.762; P < 0.01). The isolated populations in the UK have, on average, lower genetic diversity (allelic richness, proportion of loci that are polymorphic, gene diversity) than Scandinavian populations, and this diversity difference is associated with the smaller census size and population area of UK populations. From a conservation perspective, the naturally inbreeding nature of the species may buffer the species against immediate effects of inbreeding depression, but the markedly lower levels of genetic diversity in UK populations may represent a genetic constraint to evolutionary change. In addition, the high levels of population differentiation suggest that gene flow among populations will not be effective at replenishing lost variation. We thus recommend supporting in situ conservation management with ex situ populations and human-mediated seed dispersal among selected populations in the UK.     

High genetic diversity in an endangered medicinal plant, <Emphasis Type="Italic">Saussurea involucrata</Emphasis> (<Emphasis Type="Italic">Saussurea</Emphasis>, Asteraceae), in western Tianshan Mountains,China

Saussurea involucrata (Asteraceae) is a medicinal and second-degree national priority endangered plant that is mainly distributed in the high latitude region of the western Tianshan Mountains. The population is fragmented and isolated, and extensive human impact merits a suitable and specific conservation strategy, which can be compiled based on the genetic diversity, population structure, and demographic history. Phylogeographic studies were conducted on a total of five natural populations and 150 individuals were sampled. Data from three cpDNA intergenic spacer regions (trnL-F, matK, and ndhF-rpl32) and nrDNA ITS sequences showed that twelve haplotypes in cpDNA and five haplotypes in nrDNA indicated high genetic diversity among populations sampled (H _T?=?0.820 and 0.756) and within populations sampled (H _S?=?0.792 and 0.721). Additionally, the high genetic diversity did not mirror genetic structure in either cpDNA (F _ST?=?0.03153, G _ST?>?N _ST, p?<?0.05) or nrDNA (F _ST?=?0.03666, meaningless G _ST and N _ST). Two groups (north and south) were determined for a SAMOVA analysis. Based on this analysis, the demographic history was conducted with a Bayesian Skyline Plot and Isolation with Migration analysis, which showed sustainable and stable extension without a marked bottleneck. Divergence time was indicated at c. 6.25 Mya (90%HPD: 15.30–0.22 Mya) in the Miocene, which is consistent with the formation of the Kelasu section of Tianshan. The southern populations in the Bayanbulak and Gonglu regions require additional attention and transplanting would be an effective way to restore rare cpDNA haplotypes, increase effective population size, and migration rate. Our results suggested that in situ conservation of S. involucrata in western Tianshan should be the main strategy for protection and recovery of the species.     

Genetic diversity and population structure of Chinese <Emphasis Type="Italic">Lentinula edodes</Emphasis> revealed by InDel and SSR markers

Genetic diversity and population structure of 88 Chinese Lentinula edodes strains belonging to four geographic populations were inferred from 68 Insertion-Deletion (InDel) and two simple sequence repeat (SSR) markers. The overall values of Shannon’s information index and gene diversity were 0.836 and 0.435, respectively, demonstrating a high genetic diversity in Chinese L. edodes strains. Among the four geographic populations, the Central China population displayed a lower genetic diversity. Multiple analyses resolved two unambiguous genetic groups that corresponded to two regions from which the samples were collected—one was a high-altitude region (region 1) and the other was a low-altitude region (region 2). Results from analysis of molecular variance suggested that the majority of genetic variation was contained within populations (74.8 %). Although there was a strong genetic differentiation between populations (F _ST ?=?0.252), the variability of ITS sequences from representative strains of the two regions (<3 %) could not support the existence of cryptic species. Pairwise F _ST values and Nei’s genetic distances showed that there were relatively lower genetic differentiations and genetic distances between populations from the same region. Geographic distribution could play a vital role in the formation of the observed population structure. Mycelium growth rate and precocity of L. edodes strains displayed significant differences between the two regions. Strains from region 2 grew faster and fructified earlier, which could be a result of adaptation to local environmental factors. To the best of our knowledge, this was the first study on the genetic structure and differentiation between populations, as well as the relationship between genetic structure and phenotypic traits in L. edodes.     

Genetic assessment of <Emphasis Type="Italic">Abies koreana</Emphasis> (Pinaceae), the endangered Korean fir,and conservation implications

To establish a management plan for endangered and rare species, genetic assessment must first be conducted. The genetic characteristics of plant species are affected by demographic history, reproductive strategy, and distributional range as well as anthropological effects. Abies koreana E. H. Wilson (Pinaceae), Korean fir, is endemic to Korea and found only in sub-alpine areas of the southern Korean Peninsula and Jejudo Island. This species has been designated as critically endangered by the International Union for Conservation of Nature due to a continuous decline in its range and population fragmentation. We genotyped 176 individuals from seven natural populations and two afforested populations on the Korean Peninsula using 19 microsatellite loci. STRUCTURE analysis revealed two genetic clusters in natural populations (F _st  = 0.040 and R _st  = 0.040) despite low differentiation. We did not detect a significant reduction in genetic diversity or the signature of a genetic bottleneck despite population fragmentation and small population size. We deduced that this species exhibits a metapopulation structure, with the population on Jirisan Mountain acting as a source of genetic diversity for other local small populations on the Korean Peninsula, through contemporary asymmetric gene flow. However, the majority of afforested individuals on the Korean Peninsula originated from a different gene cluster. Thus, we recommend a conservation strategy that maintains two genetically unique clusters.     

Population and Conservation Genetics in an Endangered Lemur, <Emphasis Type="Italic">Indri indri</Emphasis>, Across Three Forest Reserves in Madagascar

Population decline and fragmentation often lead to reduced genetic diversity and population differentiation. Habitat destruction throughout Madagascar has caused population decline and extinction of many endemic species. Lemur populations, including those of the largest extant lemur, Indri indri, have been fragmented into remaining forest patches. We assessed the level of genetic diversity in indri populations in three protected reserves by genotyping a total of 43 individuals at 17 microsatellite loci. Genetic diversity in terms of heterozygosity was high in all three reserves, with no differences between reserves. Population structure and F _ST analyses revealed Analamazaotra Forest Station and the Torotorofotsy Conservation Area, which are separated by ca. 18 km to be genetically differentiated from each other with some admixture. Betampona Strict Nature Reserve, which is separated from the other reserves by ca. 130 km, exhibited clear population genetic differentiation, with no signs of admixture with the other reserves. Our genetic diversity estimates are similar to those for other Indridae in similar habitats and may reflect past rather than current population processes, given that populations have declined recently. Our results suggest that Betampona may be genetically isolated and that it is important to maintain gene flow between remaining populations to prevent loss of genetic diversity for the future conservation of Indri indri.     

Genetic diversity and population structure of <Emphasis Type="Italic">Melia azedarach</Emphasis> in North-Western Plains of India

Key message

Genetic structure among M. azedarach populations was detected and two subpopulations were present among them. A significant ‘isolation by distance’ was found in M. azedarach population in North-Western Plains of India.

Abstract

Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na = 5.1, Ho = 0.506, He = 0.712, I = 1.386) was assessed. The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K = 2). AMOVA exhibited 73 % variation within populations and 12 % variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy = 0.365, P = 0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India.

     

An interstate highway affects gene flow in a top reptilian predator (<Emphasis Type="Italic">Crotalus atrox</Emphasis>) of the Sonoran Desert

Roads can substantially impact the population connectivity of a wide range of terrestrial vertebrates, often resulting in loss of genetic diversity and an increase of spatial genetic structure. We studied the Western Diamond-backed Rattlesnake (Crotalus atrox), a large and abundant venomous predator, to test the hypothesis that a large and relatively new roadway in Arizona (Interstate Highway I-10) is a barrier that impacts gene flow and population genetics via habitat fragmentation. Based on 72 C. atrox sampled from three specific sampling sites (“subpopulations”) on both the west and east corridors of I-10, we used 30 nuclear microsatellite DNA loci and three mitochondrial DNA genes (2615 bp) to assess genetic diversity and structure, estimate effective population size (N _e ), and describe patterns of gene flow. We found no evidence for loss of genetic diversity or a decrease in N _e between the three subpopulations. Our microsatellite analysis showed that two subpopulations in close proximity (4 km), but separated by I-10, showed greater levels of genetic differentiation than two subpopulations that were separated by a greater distance (7 km) and not by I-10 or any other obvious barriers. Mitochondrial DNA analyses showed no significant genetic differentiation nor any indication of historically impeded gene flow. Tajima’s D and mismatch distribution tests revealed that demographic expansion is occurring in the overall population (all three subpopulations). Bayesian clustering and spatial genetic autocorrelation analyses of microsatellite data showed resistance to gene flow at the approximate location of I-10. Simulations that investigated gene flow between the subpopulations (with and without a highway barrier present) were consistent with our molecular results. We conclude that I-10 has reduced gene flow in a population of an important reptilian predator of the Sonoran Desert in southern Arizona and make conservation recommendations for reversing this trend.     

Geographic and temporal genetic structure in <Emphasis Type="Italic">Lepeophtheirus salmonis</Emphasis> from four salmon farms along the northwest and west coasts of Ireland: results from a microsatellite analysis

The marine ectoparasitic copepod of salmonids, Lepeophtheirus salmonis (Krøyer), is a major pest of farmed Atlantic salmon (Salmo salar L.) causing great economic impact. The spatial scales over which L. salmonis populations in different salmon farms are typically connected, and the temporal scales over which L. salmonis from the same farm typically undergo genetic change are largely unknown. These questions were posed in a small-scale geographic study of population structure in L. salmonis from four salmon farms, along the northwest and west coasts of Ireland, using two outgroups from Norway and Canada. The temporal stability of genetic composition was also studied in samples collected quarterly during one year from one salmon farm in Ireland. Genetic composition in L. salmonis was characterised using four nuclear microsatellites. Significant but low genetic differentiation was observed between all sites (F _ST = 0.08), with no evidence that differentiation was correlated with geographic distance. Temporal genetic differentiation was also evident (F _ST = 0.07). An analysis of all L. salmonis samples except the ones from Norway detected two separate clusters. Each cluster contained both geographical and temporal samples. These results are consistent with a population model in which L. salmonis in salmon farms along the northwest and west coasts of Ireland are not isolated, but are potentially subject to (i) localised ecological factors at the particular farm sites or (ii) selection post-settlement or a combination thereof.