Article

GENALEX 6: Genetic Analysis in Excel. Population genetic software for teaching and research

March 2006
Molecular Ecology Notes 6(1):288-295

March 2006
6(1):288-295

DOI:10.1111/j.1471-8286.2005.01155.x

Authors:

Australian National University

GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/

Population structure and diversification of Gymnospermium kiangnanense , a plant species with extremely small populations endemic to eastern China

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Jun 2024

Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium . Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense . Methods A total of 143 individuals from eight extant populations of G. kiangnanense , including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity ( He = 0.179, I = 0.286), but a high degree of genetic differentiation ( F ST = 0.521). The mean value of gene flow ( N m ) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense .

Population structure and plastron shape variability of European pond turtles (Emys orbicularis) in the Comunitat Valenciana, Spain

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Jun 2024

Unraveling the complex biogeographic and anthropogenic history of mountain goats ( Oreamnos americanus ) in Alaska

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Jun 2024

Both natural and anthropogenic forces can play a substantial role in the demographic history and current structure of a wildlife population. Species with strict habitat requirements are especially susceptible to these impacts. Mountain goats (Oreamnos americanus) in Alaska are of particular interest in this regard due to their influence on alpine ecosystems, importance to human cultures, and enigmatic history in some areas. Here, we used genetic tools to examine the population structure and demographic history of mountain goats in Alaska. We genotyped 816 mountain goats at 18 microsatellites, identified the number of genetically distinct subpopulations, and assessed their genetic diversity. We used Bayesian methods to investigate demographic history relative to the known geologic and human history of Alaska, and we simulated human-mediated translocation events onto islands to address the hypothesis that Baranof Island harbored an extant population prior to an early 20th-century introduction. We showed that Alaska has 4 genetically distinct subpopulations of mountain goats. The main demographic split between Southcentral and Southeast Alaska occurred following the retreat of ice after the Last Glacial Maximum. Simulations of translocation events largely aligned with expected genetic diversity patterns of current subpopulations except for Baranof Island which showed greater diversity than the simulation, consistent with the hypothesis of an endemic population prior to the translocation. This study highlights the value of considering both natural and anthropogenic forces when assessing the biogeographic history of a species and provides new insights about the complex demographic history and biogeography of mountain goats in Alaska.

Variabilidade genética de Aedes aegypti (diptera: culicidae) do semi-árido paraibano

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Jun 2024

A eficiência de um programa de controle do Aedes aegypti depende do conhecimento sobre genéticas que ocorrem entre as suas populações. A presente pesquisa teve por objetivo comparar variabilidade genética entre populações de A. aegypti coletadas em diferentes regiões do semiárido paraibano. A análise da estrutura gênica das populações foi realizada através das Extrações de DNAs totais e análise por RAPD-PCR. Os índices de variabilidade genética apresentaram maior diversidade na população de Barra de Santana (P = 93,33 %; Ho = 0,373) e o menor na população de Cuité (P = 60,00%; Ho = 0,171). Em função dos resultados verificou-se que há um padrão diferenciado de desenvolvimento entre as populações de A. aegypti procedentes de diferentes municípios do semiárido paraibano. Os índices de diversidade genética heterozigosidade Ho e polimorfismos sugerem elevada variação genética intrapopulacional e baixa variabilidade interpopulacional. Tal fato pode indicar constantes migrações de vetores para essas localidades com elevado número de indivíduos.

Population genetic insights into the conservation of common walnut (Juglans regia) in Central Asia

Article

Jun 2024

Studies on host plant resistance in barley (Hordeum vulgare L.) against corn leaf aphid Rhopalosiphum maidis (Fitch)

Thesis

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Jul 2022

Sunny Maanju

The present study titled “Studies on host plant resistance in barley (Hordeum vulgare L.) against corn leaf aphid Rhopalosiphum maidis (Fitch)” was carried out at the Entomology Laboratory and Research Farm of ICAR-IIWBR, Karnal during rabi, 2021-22. A total of 152 barley genotypes including 109 cultivated and 43 wild genotypes were screened in the glasshouse against R. maidis and categorized on the basis of number of aphids per shoot, intensity of leaf chlorosis and leaf rolling symptoms. These all genotypes were further characterized on the basis of genetic diversity data generated using 10 SSR polymorphic R. maidis specific primers through modified CTAB DNA extraction protocol, polymerase chain reaction (PCR) amplification and running the amplified products in 3% horizontal agarose gel electrophoresis to obtained bands. The genotypic data so generated was used for population structure analysis of all the 152 barley genotypes using various molecular data analysis softwares viz., STRUCTURE, STRUCTURE Harvester, Gene-Calc, GenAlEx, NTSYS-pc and DARwin. Out of the 152, three cultivated barley genotypes namely DWRB 123, DWRB 137 and Alfa 93, were selected for further investigation on silicon induced host plant resistance against R. maidis. The two-preference test using plant-detached leaves from three selected barley genotypes i.e., Free choice test and Pair choice test against R. maidis were carried out along with an experiment of silicon content determination from the same leaf samples used in the two preference tests. Based on the varietal screening, the wild assession IG 144114 (1.56 mean aphid population) was found to be have maximum resistance against R. maidis, while Alfa 93 was highly preferred, with 89.74 mean number of aphids per shoot. In the genetic characterization experiment, the 10 polymorphic simple sequence repeat (SSR) markers contained 70 different alleles ranging from 3 to 12 alleles per marker with an average value of 7.0 alleles per marker. The maximum and minimum Heterozygosity and Polymorphic Information Content (PIC) was observed in the primer SSR27 and SSR28, respectively. The STRUCTURE software revealed the presence of 5 different sub-populations (K=5) among all the 152 genotypes. While, based on the results AMOVA, there was 32% and 68% variation among and within the five different sub-populations. Comparison of phenotypic (varietal screening) and genotypic data (STRUCTURE and NTSYSpc 2.0 software), revealed 13 different clusters of 35 genotypes including IG 144114 with similar resistant reactions against R. maidis which can be further utilized in the aphid resistance breeding programs. The results of PCoA and radial tree diagram from DARwin software confirmed the results of other clustering methods. Although, there was mixed effect of different silicon treatments of varying concentrations on R. maidis in barley under Free choice test, in spite of confirmed Si deposition in leaf samples. However, 1% foliar spray of K2 SiO3 (potassium silicate) imparted maximum resistance with least aphid population and highest percent reduction in aphid population over untreated control under Pair choice test.

SSR marker-based individual identification system to trace illegal logging and geographic origin of teak ( Tectona grandis L.f.) wood in India

Article

Jun 2024

Illegal tree felling is one of the crucial problems in forestry worldwide. It is essential to develop adequate forensic techniques that can verify the origin of timber sourced at logging concessions. Teak wood—one of the most important timber species in India—is often illegally logged and also imported from other countries without certification. In our study, the best combination of Simple Sequence Repeat (SSR) markers identified was utilized for match testing the genetic profiles of seized and evidence woods. A genetic reference database was also developed to assign unknown wood samples to their source populations. Our results found a perfect match between the genetic profiles of seized wood and their respective evidence wood which ascertains the utility of genetic profiles as an efficient forensic tool. Further, efficiency of assignment tools based on different approaches such as distance-based, model-based and machine learning were tested. Mycorrhiza, a machine learning algorithm, was identified as the best assignment tool. However, only broad provenance-level assignment was possible due to the genetic admixture in a few natural teak populations. Mycorrhiza was then used to identify the origin of two plantations in India. The assignment test predicted that both the plantations had similar origin, having sourced seeds from multiple natural populations (through clonal seed orchards and seed production areas) and local populations in different ratio. The SSR markers and assignment tool from this study can be used as an effective forensic tool to curb illegal felling and to verify integrity of timber supply chains in India. Also, provenance-based assignment guarantees usage of these markers in a global scale. However, a collective global effort to develop and deposit a robust reference database in a common repository is a prerequisite to strengthen timber traceability worldwide.

Clonality and limited population diversity of Fusarium circinatum in Colombia

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Jun 2024
FOREST PATHOL

Fusarium circinatum is an important fungal pathogen of Pinus species utilized in commercial forestry worldwide. In Colombia, it was first found on nursery plants and later in plantations associated with basal cankers on young trees. In this study, we explored the population diversity of the pathogen in Colombia by analyzing 136 isolates collected from diseased nursery plants (2005–2007) and plantation trees (2017 and 2020).These were sourced from different geographical regions and Pinus species. Genotyping was performed using 10 microsatellite markers, while mating types were identified with PCRs targeting the MAT1 locus. Using microsatellites, a total of 33 multilocus haplotypes were detected. Genetic diversity indices showed low levels of diversity in both the overall collection and in specific collection groupings. The data also suggested that a small number of isolates had unique origins in the country (p < .05), and relatively low levels of population differentiation were detected between the nursery and plantation collections. All the isolates were scored as having the MAT1-1 mating type, and no evidence for the random association among microsatellite alleles (p = .0001) was found. Overall, these data suggest that F. circinatum was introduced into Colombia a small number of times, likely on seed for nursery production. Furthermore, the data also indicate that the pathogen has spread from nurseries to the plantations via asexual reproduction and on asymptomatic plants. This has resulted in a highly clonal F. circinatum population in Colombia that has resulted from accidental introductions of the pathogen into a production nursery.

Genetic diversity and population structure analysis of a diverse panel of pea (Pisum sativum)

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May 2024

Breeding resilient cultivars with increased tolerance to environmental stress and enhanced resistance to pests and diseases demands pre-breeding efforts that include understanding genetic diversity. This study aimed to evaluate the genetic diversity and population structure of 265 pea accessions. The diversity arrays technology (DArT) genotyping method was employed to identify single-nucleotide polymorphisms (SNPs) and silico markers. After stringent filtering, 6966 SNP and 8,454 silico markers were selected for diversity analysis. Genetic diversity was estimated by grouping accessions based on plant material type, geographic origin, growth habit, and seed color. Generally, diversity estimations obtained using SNPs were similar to those estimated using silico markers. The polymorphism information content (PIC) of the SNP markers ranged from 0.0 to 0.5, with a quarter of them displaying PIC values exceeding 0.4, making them highly informative. Analysis based on plant material type revealed narrow observed heterozygosity (Ho = 0.02–0.03) and expected heterozygosity (He = 0.26–0.31), with landrace accessions exhibiting the highest diversity. Geographic origin-based diversity analysis revealed Ho = 0.02–0.03 and He = 0.22 to 0.30, with European accessions showing the greatest diversity. Moreover, private alleles unique to landrace (4) and European (22) accessions were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance revealed a highly significant genetic differentiation among accession groups classified by seed color, growth habit, plant material types, and geographic origin (p < 0.01). Principal coordinate analysis and neighbor-joining cluster analysis revealed weak clustering of accessions at different grouping levels. This study underscores the significance of genetic diversity in pea collections, offering valuable insights for targeted breeding and conservation efforts. By leveraging genomic data and exploring untapped genetic resources, pea breeding programs can be fortified to ensure sustainable plant protein production and address future challenges in agriculture.

Characterization of 23 microsatellite markers and development of multiplex PCRs for the Amur viper Gloydius saxatilis (Viperidae) and cross-species amplification in other Gloydius species

Article

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Feb 2024
GENET MOL RES

The Amur viper (family Viperidae), Gloydius saxatilis (Emelianov, 1937) is found in Russia, China, and the Korean Peninsula, and suffers from considerable poaching pressure driven by financial incentives. Its unique distribution has attracted attention as an indicator species for climate change. Herein, we report the isolation and characterization of 23 novel microsatellite loci in G. saxatilis using next-generation sequencing technology consisting of six multiplex panels. We collected 42 muscle samples from G. saxatilis that had either been road-killed or captured at various natural sites in South Korea. Twenty-two samples were collected from Gangwon-do, four from Gyeonggi-do, nine from Gyeongsang-do, five from Jella-do, and two from Chungcheong-do. The observed and expected heterozygosities of the loci varied from 0.447 to 0.937 and 0.436 to 0.815, respectively. The number of alleles per locus ranged from four to 15. All loci were in Hardy–Weinberg equilibrium, and no linkage disequilibrium was detected among any pairs of the loci. Examination of cross-species amplification showed that 20 loci were transferable to two other Gloydius snakes (G. ussuriensis and G. brevicaudus) and helped in identifying each species and hybrid. The six multiplex panels of 23 polymorphic microsatellite loci will play an important role in future population genetic studies and in the conservation and management of the Gloydius species.

Colony life history of the tropical arboreal ant, Cephalotes goniodontus De Andrade, 1999

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Jun 2024
INSECT SOC

Ian Andrew Eckardt Butler

Arboreal ants are ecologically important in tropical forests, but there are few studies using DNA markers to examine their population and colony structure. Colonies of the arboreal turtle ant Cephalotes goniodontus create trail networks through the canopy of the tropical forest, in dense vegetation where it is difficult to determine how long a nest is used and how neighboring colonies partition space. We monitored 53 nest sites for up to six years and, using seven microsatellite markers, genotyped samples of workers collected at or near 41 nests over 1-4 years. We calculated average relatedness within samples collected at a given location, and between samples collected at the same location in successive years, and performed pedigree analysis to predict the number of queens that produced each sample of workers. Fifteen samples were highly related (r ≥ 0.6) from single colonies, of which 11 were monogynous and the remaining four had two queens; 19 were of intermediate relatedness (0.1 ≤ r < 0.6) with 1-6 queens, and 7 were groups of unrelated workers (r < 0.1) from at least 4 queens. Colonies persisted at the same nest site for 2-6 years. The smallest distance we found separating nests of different colonies was 16.2 m. It appears that different colonies may share foraging trails. Our study demonstrates the feasibility of using a cost-efficient genotyping method to provide information on colony structure and life history of ant species.

Genetic Analysis and Construction of a Fingerprint for Licensed Triadica sebifera Cultivars Using SSR Markers

Article

Full-text available

Jun 2024

Triadica sebifera is an important landscaping tree species because of its colorful autumn leaves. In recent years, some cultivars have been bred and licensed, but it can be difficult to identify them from their morphological traits due to their similar phenotypes. To explore the genetic relationships and construct a fingerprint of the cultivars, the licensed T. sebifera cultivars were analyzed using SSR markers. A total of 179 alleles were identified among the 21 cultivars at 16 SSR loci, and these alleles exhibited a high level of genetic diversity (He = 0.86). The genetic variations mainly occurred among cultivars based on an analysis of molecular variance (AMOVA). According to phylogenetic analysis, principal coordinate analysis (PCoA), and Bayesian clustering analysis, the genetic relationships were independent of geographic distances, which may be mainly due to transplantations between regions. Some cultivars with different leaf colors showed obvious genetic differentiation and may be preliminary candidates for cross-breeding. Finally, the fingerprint for the licensed cultivars was constructed with two SSR markers. The results of this study can provide technical support for the application and legal protection of licensed Triadica sebifera cultivars.

Hybridization and introgression of two sympatric Lycium species revealed by simple sequence repeat (SSR) markers

Article

Full-text available

Jun 2024
GENET RESOUR CROP EV

Hybridization and introgression are important ways to promote genetic variation and play important roles in the evolution of species. Two sympatric Lycium populations, L. ruthenicum and L. barbarum, are found in the Qiadam Basin. In this study, we sampled 30 trees and analyzed the phenotypic characteristics of tree shape, leaf type, and fruit type. In addition, we analyzed these samples using generic simple sequence repeat (SSR) markers. The molecular marker data revealed that direct gene flow between the two Lycium species was fairly low, while the gene flow between hybrids and parents was greater; therefore, the majority of gene introgression was intermediate because of the backcrossing of hybrids with the two parents. Structure analysis revealed that L. ruthenicum maintained a stricter genetic boundary than did L. barbarum, and compared with L. ruthenicum, L. barbarum was found to backcross with the hybrids more intensively, consistent with the fruit morphological observation. The introgression ability of the studied alleles varied across species, with some being completely blocked from interspecific introgression. Our study provides a theoretical foundation for Lycium breeding and a practical example for understanding the evolution of Lycium species.

Deciphering genetic diversity and population structure in ex-situ conserved Brassica rapa var. yellow sarson germplasm using morphological traits and simple sequence repeat (SSR) markers

Article

Full-text available

Jun 2024
GENET RESOUR CROP EV

Brassica rapa (2n = 20, AA) is consumed as vegetable, fodder and oilseed crop. Oilseed type B. rapa species occupy important place after B. juncea in India. So, present study was carried out to study genetic diversity and population structure in 136 yellow sarson germplasm using 17 morphological traits and 99 simple sequence repeat (SSR) markers. A good frequency for most of the morphological traits was reported. At species level, morphological markers exhibited maximum polymorphism (61.89%) as compared to SSR markers (46.67%). Analysis of molecular variance (AMOVA) revealed significant differences among populations based on different markers. However, SSR markers (PhiPT = 0.040, p-value = 0.010) revealed more variation between populations as compared to morphological traits. On the basis of pooled markers, indigenous lines showed highest expected heterozygosity (He = 0.20) and polymorphism (P = 87.96%). Both markers revealed lowest Nei’s genetic distance (GD) between advanced breeding lines and indigenous lines (Morph GD = 0.01, SSR GD = 0.01). Furthermore, optimum three clusters (K = 3) were deciphered in yellow sarson germplasm based on principal coordinates analysis (PCoA), AMOVA and population structure analysis. PCoA and AMOVA could be used in addition to delta K and LnPd in deciding optimum number of clusters in structure analysis. Information of present study will be useful in selection of suitable traits and SSR markers for characterization, conservation and utilization of yellow sarson germplasm. Likewise, inclusion of more number of morphological characters, seed biochemical parameters and genotyping by sequencing would be helpful in gaining more understanding on genetic variability and diversity of these traits in yellow sarson.

GENETIC AND FISH-BREEDING BIOLOGICAL RESEARCH ON STURGEON SPECIES FOR THE PURPOSE OF ARTIFICIAL REPRODUCTION

Article

Jun 2024

The results of the spawning campaign using producers of beluga and Russian sturgeon, whose offspring were grown in industrial conditions and released into a water body of fishery importance, are considered. A genetic and fish-breeding-biological assessment of producers of sturgeon species for the purposes of artificial reproduction is given. Indicators of genetic characteristics of fish producers have been revealed. It has been determined that beluga producers have a reason for If the homozygosity of the species is high, it is necessary to carefully select parent groups taking into account the genetic characteristics of individuals to avoid closely related crosses and to use parental pairs rather than groups. Due to the high number of breeders, Russian sturgeon producers have a choice that allows them to take pairs of individuals with the least number of common alleles to obtain genetically diverse offspring. Fishbreeding and biological studies of beluga producers showed a tendency to reduce reproductive indicators depending on the number of generations in factory conditions, in Russian sturgeon producers the indicators of females with the second and third generations of offspring were almost identical, with slight deviations from each other. The practical significance is determined in the rational and effective use of the fish-breeding and genetic potential of producers in order to obtain the most genetically diverse juveniles, which will ultimately have a positive impact both on the preservation of the gene pool of sturgeon populations and on the survival of offspring at the rearing stage.

Genetic diversity and population dynamics of wild Mozambique tilapia (Oreochromis mossambicus) in South Africa

Article

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Jun 2024

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

Article

Full-text available

Jun 2024

The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean F st=0.016), with greater separation evident between geographically distant sites (F st range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.

Ocean circulation contributes to genetic connectivity of limpet populations at deep‐sea hydrothermal vents in a back‐arc basin

Article

Full-text available

Jun 2024
EVOL APPL

For endemic benthos inhabiting hydrothermal vent fields, larval recruitment is critical for population maintenance and colonization via migration among separated sites. The vent‐endemic limpet, Lepetodrilus nux, is abundant at deep‐sea hydrothermal vents in the Okinawa Trough, a back‐arc basin in the northwestern Pacific; nonetheless, it is endangered due to deep‐sea mining. This species is associated with many other vent species and is an important successor in these vent ecosystems. However, limpet genetic diversity and connectivity among local populations have not yet been examined. We conducted a population genetics study of L. nux at five hydrothermal vent fields (maximum geographic distance, ~545 km; depths ~700 m to ~1650 m) using 14 polymorphic microsatellite loci previously developed. Genetic diversity has been maintained among these populations. Meanwhile, fine population genetic structure was detected between distant populations, even within this back‐arc basin, reflecting geographic distances between vent fields. There was a significant, positive correlation between genetic differentiation and geographic distance, but no correlation with depth. Contrary to dispersal patterns predicted by an ocean circulation model, genetic migration is not necessarily unidirectional, based on relative migration rates. While ocean circulation contributes to dispersal of L. nux among vent fields in the Okinawa Trough, genetic connectivity may be maintained by complex, bidirectional dispersal processes over multiple generations.

Molecular characterization by two types of DNA markers for indigenous ducks in Kurdistan

Article

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Jan 2024

Genetic diversity, population structure and demographic history of the rock oyster Striostrea prismatica (Gray, 1825) within two Eastern Pacific biogeographic realms

Article

Jun 2024
MAR FRESHWATER RES

Anthropogenic dispersal explains the phylogeography of insular edible dormouse Glis glis in the Mediterranean basin

Article

Full-text available

Jun 2024

The history of human colonisation in the Mediterranean has long been recognised as a crucial factor influencing biodiversity patterns in southern Europe. Nonetheless, our understanding of how anthropogenic and natural dispersal events interacted in shaping wildlife distributions, particularly in small mammals, remains limited. The edible dormouse Glis glis, a widespread European species, whose distribution includes several islands in the Mediterranean, present an opportunity to investigate these interactions. In this work, we used the edible dormouse to test hypotheses regarding the interplay between natural and anthropogenic dispersal in shaping species' distributions in Mediterranean archipelagos. We compared genetic sequences from samples collected on Mediterranean islands (Elba Island, Corsica, Sardinia, Sicily and Salina Island) and the mainland. Twenty-one samples were analysed by amplifying and sequencing a fragment of the cytochrome oxidase subunit I gene. Results indicated that samples from Sardinia and Elba Island belong to the same clade of mainland Italy, specifically to the subspecies G. g. italicus. This finding does not support the existence of an endemic Sardinian subspe-cies and suggests recent introduction events. In contrast, Salina Island only included individuals belonging to the Sicilian subspecies, whereas Sicily hosts a mixed population of G. g. italicus and G. g. insularis. The Corsican population likely originated from a different stock than Sardinia, possibly originating from Northern Italy or southern France. Overall, our findings underscore the significant role of anthropogenic dispersal in shaping the current distribution of the edible dormouse on islands.

Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China

Article

Full-text available

Jun 2024
BMC PLANT BIOL

Background The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China. Results We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region. Conclusion Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene–Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China’s secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.

Genetic structure and diversity of the island-endemic freshwater prawn Macrobrachium shokitai Fujino & Baba, 1973 (Decapoda: Caridea: Palaemonidae) on Iriomote Island, Ryukyu Archipelago, southern Japan

Article

Jun 2024

Iriomote Island is a small continental island hosting approximately 40 rivers characterized by short, steep-gradient streams and small waterfalls. We examined the population genetic structure and diversity of the freshwater prawn Macrobrachium shokitaiFujino & Baba, 1973 (Palaemonidae) using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Specimens were collected from 19 sites along ten rivers on the island, covering the known geographic distribution of the species. Haplotype and nucleotide diversities were very low within each river on the island. Nearly all haplotypes were exclusive to a given river, confirming distinct population structures among rivers at a small geographical scale. Slight genetic differentiation was discerned between the upper and lower sites of waterfalls in only the Yuchin River. Phylogenetic tree reconstruction, haplotype network, and principle coordinate analysis classified five clades roughly correspond to geographical groups in the western, southern, central, and northern regions of the island. Extreme caution should therefore be taken when translocating individuals to other rivers to avoid introducing genetic disturbance, even during conservation and mitigation efforts.

City divided: Unveiling family ties and genetic structuring of coyotes in Seattle

Article

Jun 2024

Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non‐urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote ( Canis latrans ) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.

Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses

Article

Full-text available

Jun 2024
TROP ANIM HEALTH PRO

This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world’s youngest (geo-dynamically sensitive) mountain system, “the Himalayas”. Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand’s domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.

Genetic connectivity and diversity between tropical and subtropical populations of the tropical horned sea star Protoreaster nodosus in the northwest Pacific

Article

Full-text available

Jun 2024
MAR BIOL

Seagrass beds are ecologically and economically important coastal ecosystems, and seagrass-associated organisms are a key part of their biodiversity. Marine organisms that reproduce through broadcast spawning are likely to have less genetic differentiation among populations than those that use other modes of reproduction, but this has not been well studied. Here, we investigated the genetic diversity, genetic differentiation, and migration patterns of the seagrass-associated sea star Protoreaster nodosus across 12 sites spanning approximately 2500 km from the Ryukyu Archipelago, Japan, to the Philippines. We genotyped 405 individuals by using seven microsatellite loci and analyzed allelic richness and expected heterozygosity as indices of genetic diversity. Of these two indices, only expected heterozygosity decreased slightly with increasing latitude. These results suggest that genetic diversity has not clearly decreased, even in the isolated Ryukyu Archipelago populations. Geographic distance was significantly correlated with genetic differentiation (pairwise FST: − 0.005 to 0.049). However, populations in the Ryukyu Archipelago and the Philippines showed relatively low genetic structuring and the pairwise genetic differentiation between these regions was often non-significant. Analysis of historical migration rates showed bidirectional north–south migration, which appears to be influenced by the Kuroshio Current and its countercurrents.

Molecular characterization of a distinct ginger chemotype from Thua Thien Hue, Vietnam, and the application of PCR-based markers for identifying unknown ginger populations in the region using machine learning

Article

Full-text available

Jun 2024

Ginger ( Zingiber officinale Roscoe) stands as an esteemed herbaceous spice due to its extensive applications in medical and culinary sectors. The variety of ginger indigenous to Thua Thien Hue, known as Hue's ginger, has long garnered recognition for its distinct aroma and unique oil composition. Regrettably, this ginger variety has intermingled with unidentified ginger types. Thus, the objective of this study is to identify DNA markers that can facilitate the identification of Hue's ginger. Such markers will enable the precise selection and preservation of the authentic ginger chemotype. To substantiate the distinctive genetic attributes of Hue's ginger, we employed two marker techniques: RAPD and mat K DNA barcoding. The RAPD technique demonstrated its robustness by generating an impressive number of 139 amplicons, with an absolute polymorphic rate of 100%. Among the resulting bands, two region-specific markers, OPA03-480 and OPB01-1150, were delineated for Hue's ginger. These specific markers facilitated the separation of Hue's ginger from other ginger chemotypes, shown by principal coordinates analysis. Furthermore, the alignment of the mat K gene sequence of Hue's ginger with the reference chloroplast genome substantiated the hypothesis that Hue's ginger possesses distinct genetic characteristics. This alignment revealed three transition variants within the matK gene of Hue’s ginger. Considering the extensive intermixing of ginger populations in Thua Thien Hue, we constructed an XGBoost machine-learning model using RAPD data to identify the most pivotal markers capable of effectively distinguishing between these populations. Our model identified OPN06-350, OPA03-480, OPD02-500, OPF04-950, and OPN06-300 as the most influential markers for population discrimination. This study not only furnishes molecular markers for the precise identification of a unique Vietnamese ginger chemotype but also advocates for the utilization of machine-learning methodologies employing PCR-based marker data for the identification of pivotal markers, a practice with promising implications for the effective differentiation of plant varieties in future endeavors.

DNA bar-coding of plant growth promoting strains of Trichoderma

Research

Full-text available

Oct 2023

Guiding Seed Movement: Environmental Heterogeneity Drives Genetic Differentiation in Plathymenia reticulata Benth., Providing Insights for Restoration

Article

Full-text available

May 2024

Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic, and spatial distance factors on the genetic patterns of Plathymenia reticulata Benth., aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil, and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).

Genetic differentiation at extreme latitudes in the socially plastic sweat bee Halictus rubicundus

Article

Full-text available

May 2024
PLOS ONE

The sweat bee Halictus rubicundus is an important pollinator with a large latitudinal range and many potential barriers to gene flow. Alongside typical physical barriers, including mountain ranges and oceans, the climate may also impose restrictions on gene flow in this species. The climate influences voltinism and sociality in H. rubicundus, which is bivoltine and can nest socially at warmer lower latitudes but tends to be univoltine and solitary in the cooler north. Variation in voltinism could result in phenological differences, potentially limiting gene flow, but a previous study found no evidence for this in H. rubicundus populations in mainland Britain. Here we extend the previous study to consider populations of H. rubicundus at extreme northern and southern latitudes in the UK. We found that bees from a population in the far north of Scotland were genetically differentiated from bees collected in Cornwall in the south-west of England. In contrast, bees collected across the Irish Sea in Northern Ireland showed slight genetic overlap with both the Scottish and Cornish bees. Our results suggest that when populations at extreme latitudes are considered, phenology and the climate may act alongside physical barriers such as the Scottish Highlands and the Irish Sea to restrict gene flow in H. rubicundus. We discuss the implications of our results for local adaptation in the face of rapidly changing selection pressures which are likely under climate change.

Genetic and phenotypic differentiation in functional traits of Iris pseudacorus L. in native and introduced Mediterranean climate ranges

Article

Full-text available

May 2024
BIOL INVASIONS

Intraspecific variation in functional traits between native and introduced plant species may underlie resilience and invasiveness of introduced species. We explored if observed phenotypic variation of Iris pseudacorus L. between populations in the native vs. introduced ranges results from genetic differentiation and/or phenotypic plasticity. Seeds were collected from populations along estuarine stress gradients within populations in both Guadalquivir Estuary (Andalusia, Spain) and San Francisco Bay-Delta Estuary (California, USA). Genetic analysis was performed on leaf tissue from plants in each seed donor population. Germinants (n = 48: 6 plants × 4 populations × 2 ranges) were grown for 12 months in a common garden experiment (CGE). We then evaluated 25 traits including growth, biomass allocation, morphological and biochemical responses. Geographic range explained relative intraspecific trait variation segregating native from introduced phenotypes. Native plants had lower specific leaf area (− 34%) and carbohydrate concentrations in rhizomes (− 63%) than introduced plants, providing evidence of genetic differentiation. Higher genetic diversity and 27% higher phenotypic variation (CGE) of native vs. introduced plants indicated longer-term adaptive processes in the native range. Genetic distance of introduced populations (field) increased along with their phenotypic distance (CGE), suggesting rapid genetic differentiation. Phenotypic plasticity also explained some observed inter-range differences under field conditions not expressed by plants in the CGE. Management of the introduced I. pseudacorus populations should be established urgently since they represent novel genotypes with key functional traits that can support invasiveness through increased competitive ability and physiological stress tolerances to sea level rise.

Genetic Differentiation and Clonality in a Local Population of the Caucasian Endemic Trifolium polyphyllum C.A. Mey. (Fabaceae)

Article

Full-text available

May 2024
Genetika

Trifolium polyphyllum is a Caucasian endemic of the Fabaceae family peculiar for its inability of nitrogen fixation. Despite this unique trait, the species is insufficiently studied, in particular, little is known about its propagation and dispersal modes. Analyses of ISSR markers in a sample from a population at Malaya Khatipara Mountain revealed that the species is capable to both sexual and vegetative propagation; however, the former mode dominates. We found out that separate patches within a local population are considerably genetically differentiated within an area of about 2000 square meters (PhiPT = 0.349; p = 0.001). We suppose this may happen due to lack of adaptations to seed dispersal. We also suppose that the observed concentration of genetically admixed individuals in upper parts of slopes is due to peculiarities of pollinators’ behavior. The size of vegetative clones does not exceed 1 square meter.

Genetic analysis of harvest samples reveals population structure in a highly mobile generalist carnivore

Article

Full-text available

May 2024

Delineating wildlife population boundaries is important for effective population monitoring and management. The bobcat (Lynx rufus) is a highly mobile generalist carnivore that is ecologically and economically important. We sampled 1225 bobcats harvested in South Dakota, USA (2014–2019), of which 878 were retained to assess genetic diversity and infer population genetic structure using 17 microsatellite loci. We assigned individuals to genetic clusters (K) using spatial and nonspatial Bayesian clustering algorithms and quantified differentiation (FST and GST″$$ {G}_{\mathrm{ST}}^{{\prime\prime} } $$) among clusters. We found support for population genetic structure at K = 2 and K = 4, with pairwise FST and GST″$$ {G}_{\mathrm{ST}}^{{\prime\prime} } $$ values indicating weak to moderate differentiation, respectively, among clusters. For K = 2, eastern and western clusters aligned closely with historical bobcat management units and were consistent with a longitudinal suture zone for bobcats previously identified in the Great Plains. We did not observe patterns of population genetic structure aligning with major rivers or highways. Genetic divergence observed at K = 4 aligned roughly with ecoregion breaks and may be associated with environmental gradients, but additional sampling with more precise locational data may be necessary to validate these patterns. Our findings reveal that cryptic population structure may occur in highly mobile and broadly distributed generalist carnivores, highlighting the importance of considering population structure when establishing population monitoring programs or harvest regulations. Our study further demonstrates that for elusive furbearers, harvest can provide an efficient, broad‐scale sampling approach for genetic population assessments.

Sex-mediated gene flow of grayfoot chacma baboons (Papio ursinus griseipes) in a highly seasonal habitat in Gorongosa National Park

Preprint

Full-text available

Jun 2024

Investigating primates’ behavioral variation at the inter-population level is important for the understanding of the evolutionary processes leading to species-specific patterns. The study of behavioral diversity among populations also contributes to improving’ primate conservation efforts. Dispersal patterns tend to be similar among close phylogenetic lineages but may vary in response to individual-based responses. Here, we investigate dispersal patterns of chacma baboons (Papio ursinus griseipes) living in Gorongosa National Park (GNP) and the Catapu Forest Reserve (CFR) in central Mozambique. The park consists of a mosaic landscape, located in a seasonally variable area. GNP was the epicenter of a major war, which severely reduced most apex predators resulting in limited mammalian predation on baboons and a steep increase in number of groups and/or group’s fission. We used a genetic dataset of 121 non-invasive DNA samples analyzed for uni- and bi-parentally inherited markers aiming to characterize the spatial distribution of genetic variation and investigate the extent and direction of sex-mediated gene flow at different time scales. We found high levels of genetic diversity as estimated using autosomal microsatellite loci data and no evidence for a significant contraction of the population size in the last generations. A very distinct mitochondrial DNA haplotype was sampled in CFR. We found evidence for historical and instantaneous male-biased dispersal and female philopatry, estimated among localities and at short distances in GNP, respectively. Our study highlights the strong conservation of sex-biased dispersal patterns and philopatry in chacma baboons and suggests that dispersal behaviors in chacma baboons are resilient to environmental changes and seasonality.

Assessing the Genetic Diversity of Five Cattle Breeds Using SNP Markers Associated with Health

Article

Jun 2024

Assessment of diversity, population structure and gene flow in indigenous and exotic accessions of Adzuki bean (Vigna angularis Willd.)

Preprint

Full-text available

Jun 2024

Adzuki beans are recognized for their high carbohydrate content and protein composition, featuring a well-balanced amino acid profile, particularly abundant in lysine. This compensates for the typically deficient protein levels found in commonly consumed cereals. Morphological diversity analysis categorized 96 adzuki accessions into three distinct clusters, with the greatest intra-cluster distance observed between cluster I and cluster II. Principal Component Analysis indicated that PC1 accounted for 55.90% of the total variation, primarily attributed to traits such as primary branches per plant, plant height, 1000-seed weight, clusters per plant, seed yield per plant, and seeds per pod. Seventy SSR primers were utilized to assess molecular diversity. Among these, 11 primer pairs exhibited polymorphism, with a mean PIC value of 0.241. The average number of effective alleles (Ne) and Shannon’s Information Index (SII) were calculated as 1.5051 and 0.4560 per locus, respectively. Clustering analysis using the NTSYS-pc package identified three clusters comprising both indigenous and exotic accessions. Population STRUCTURE revealed the highest ΔK mean value at K = 2, dividing the 96 germplasm accessions into two distinct gene pools, consisting of pure lines and admixtures. AMOVA conducted between the two populations unveiled that 79% of the variation exists within populations, while 21% exists among populations. The pure lines and polymorphic SSR markers identified in this study hold promise for the development and evaluation of core collections and the breeding of superior varieties of adzuki beans along with harnessing genetic diversity in adzuki beans to enhance breeding endeavors toward superior varieties and hybrids.

New insights into population structure, demographic history, and effective population size of the critically endangered blue shark Prionace glauca in the Mediterranean Sea

Article

Full-text available

Jun 2024
PLOS ONE

The blue shark, Prionace glauca, is the most abundant pelagic shark in the open ocean but its vulnerability remains poorly understood while being one of the most fecund sharks. In the Mediterranean Sea, the blue shark is listed as Critically Endangered (CR) by the International Union for Conservation of Nature. The species is facing a strong decline due to fishing, and scientific data regarding its genetic structure and vulnerability are still lacking. Here, we investigated the genetic diversity, demographic history, and population structure of the blue shark within the Mediterranean Sea, from samples of the Gulf of Lion and Malta, using sequences of the mtDNA control region and 22 microsatellite markers. We also compared our mitochondrial data to previous studies to examine the Atlantic-Mediterranean population structure. We assessed the blue shark’s genetic vulnerability in the Mediterranean basin by modelling its effective population size. Our results showed a genetic differentiation between the Atlantic and the Mediterranean basins, with limited gene flow between the two areas, and distinct demographic histories making the Mediterranean population an independent management unit. Within the Mediterranean Sea, no sign of population structure was detected, suggesting a single population across the Western and Central parts of the sea. The estimated effective population size was low and highlighted the high vulnerability of the Mediterranean blue shark population, as the estimated size we calculated might not be sufficient to ensure the long-term persistence of the population. Our data also provide additional evidence that the Gulf of Lion area acts as a nursery for P. glauca, where protection is essential for the conservation strategy of the species in the Mediterranean.

Characterisation of the Cinnamomum parthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics

Article

Full-text available

Jun 2024

Cinnamomum parthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C. parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C. parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C. parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C. parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C. parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C. parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C. parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C. parthenoxylon.

Guiding seed movement: environmental heterogeneity drives genetic differentiation in Plathymenia reticulata , providing insights for restoration

Article

May 2024

Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).

Analyses of genetic diversity and population structure in Quercus griffithii Hook. f. & Thomson ex Miq. using simple sequence repeat (SSR) markers

Article

Full-text available

Jun 2024
TREE GENET GENOMES

Quercus griffithii is an ecologically and economically important tree species utilized for firewood, fodder, compost, and building-making. It is also a good source of food for wildlife. The genetic diversity of Q. griffithii is poorly understood; therefore, in the present study, 16 polymorphic SSR markers were used to assess the extent and pattern of genetic diversity in Q. griffithii samples collected from the northeastern region of India. The SSR markers revealed significant discriminating power (PIC range, 0.15˗0.81) and resulted in the amplification of 119 alleles. At the species level, it showed moderate levels of genetic diversity (Ho = 0.47; He = 0.52) with low genetic differentiation (FST = 0.06) and high gene flow (Nm = 3.91). Two genetic clusters, with high admixture populations were estimated in the Bayesian analysis of STRUCTURE, which was in accordance with clusters of UPGMA and PCoA. This is the first study to assess genetic diversity using SSR markers in Q. griffithii. The genetic information generated in this study will be helpful in the future conservation and restoration of Q. griffithii in the northeastern region of India.

Contribution of external dispersal to pollen pool genetic diversity in a riparian population of Cercidiphyllum japonicum

Article

Full-text available

Jun 2024
TREE GENET GENOMES

This study aimed to elucidate the contribution of pollen immigration to the maintenance of genetic diversity in the pollen pools received by seed parents in a riparian population of Cercidiphyllum japonicum. We estimated the pattern of potential pollen dispersal and assessed the effective number of pollen parents (Nep) and the spatial genetic structures (SGS) of pollen pools from both outside and inside the population, using the genotypes at five microsatellite loci of reproductive individuals and seeds in the population distributed along a stream. A neighborhood model approach suggested substantial pollen immigration rate (37.9%) and the fat-tailed dispersal kernel expressed as an exponential power function with a shape parameter (b) of 0.154 and a mean distance of 1,235 m, which indicated a high ability to increase Nep at locations distant from the pollen sources. Pollen pools from outside the population (outside pollen pools) genetically differed from those from inside the population (inside pollen pools), and the Nep was five times larger in the outside pollen pools (22.5) than the inside pollen pools (4.5). Furthermore, the estimate of genetic differentiation (pairwise ΦFT) between each seed parent pair in the outside pollen pools tended to be constant and much lower than that of the inside pollen pools, which may be attributed to the high genetic diversity of the outside pollen pools. Pollen immigration should contribute to genetic diversity of the population by introducing a small amount of new or low-frequent alleles and increasing the Nep of total pollen pools within the population.

Investigating Nuclear DNA Microsatellites in the Nile Tilapia (Oreochromis niloticus): Insights into Association Genetics

Article

Full-text available

Jan 2024

One of the key challenges in aquaculture is the selection of individuals with superior traits, including rapid growth rate, high flesh quality, and disease resistance. Marker-assisted selection (MAS) using molecular markers (e.g., simple sequence repeats; SSR) is known to be more effective in identifying individuals with specific traits based on their genetic makeup. The current study aimed to examine SSR markers across different linkage groups in their efficiency in characterizing the Nile tilapia fish with superior growth performance traits for usage as effective tools for MAS. A total of 152 Nile tilapia samples with identical ages but contrasting growth performances were collected from a fish farm in Kafr El-Sheik Governorate, Egypt. The collected genotypes were evaluated for growth performance metrics such as weight and length, and their microsatellite allelic patterns were also analyzed. A total of 13 microsatellite markers were assessed in the two sampled Nile tilapia categories. The t-test of growth performance traits between the two fish categories revealed highly significant differences in body weight and length. The average number of alleles per locus in the large and small populations was 2.6 and 2.2, respectively. The analyzed populations showed a significant deviation from Hardy-Weinberg equilibrium.Only seven markers showed private alleles unique to either small or large populations, indicating the suitability of these markers for association genetic studies. The studied markers showed low to moderate gene diversity (H), which ranged between 0.25 and 0.48, with an average of 0.41. The discrimination power of the studied loci was relatively high (D = 0.888). The discrepancies in growth parameters between the investigated populations were aligned with the disparities in allele frequency, indicating a possible correlation between certain allele(s) and growth performance characteristics. The present study highlighted the effectiveness of specific SSRs in addressing growth parameters during the planning for the Nile tilapia selection in breeding programs.

Occurrence and characterization of Puccinia triticina in Zimbabwe

Article

Jun 2024

Investigation of the usability of black locust (Robinia pseudoacacia L.) cultivars for feed purpose in Hungary

Preprint

Full-text available

May 2024

Nowadays, one of the major challenges in the field of agricultural production is an increasing demand for protein in farm animal husbandry. The main source of protein today is still soybean meal, but there is an urgent need to involve alternative protein sources and assess areas of application. Leaf and fruit of black locust (Robinia pseudoacacia L.) could be a possible source of protein, therefore the main composition of different varieties was examined. Black locust is the most widespread tree species in Hungary occupying approximately 24% of the forested land (465,000 ha) and providing 25% of the annual timber output of the country. The mean wood volume of all black locust forests is 125 m³/ha, with a mean volume of 190 m³/ha at the final cutting age (31 years on average). Black locust foliage could be an important, complementary feed, as it plays the role of rumen filler and during grazing, animals can access other useful plants among the trees. Foliage samples were collected from individuals of black locust cultivars, and subsequent content analyses were carried out. With the help of satellite images, photosynthetic activity and health conditions were investigated in the experimental areas using vegetation and moisture indices on the basis of content values and digestibility studies.

Microbiome and epigenetic variation in wild fish with low genetic diversity

Article

Full-text available

Jun 2024

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.

Assessment of genetic diversity of native chicken (Gallus gallus domesticus) population in Central African Republic

Article

Full-text available

May 2024

In the Central African Republic (CAR), poultry production primarily relies on indigenous chicken (Gallus gallus domesticus) as a raw genetic resource that has never been characterised despite its great genetic and economic potential in rural and periurban areas. The present study assessed the genetic diversity of native chicken in CAR using 16 microsatellite markers. Blood samples were randomly collected on FTA filter cards from 205 adult native chickens from two agroecological zones out of four in CAR, including 102 from the forest and 103 from the savannah. Sixteen microsatellite markers could amplify, giving a coverage rate of 61.54% of the SSR panel used. A low but positive Fis mean value (0.16) suggested a low inbreeding and a weak reduction in Heterozygosity of individuals due to non-random mating within each population. Overall genetic diversity (0.54), Heterozygosity (0.45) and allele frequency (0.61) confirmed a moderate to high genetic variation within the CAR indigenous chicken population. The molecular variance was more significant within individuals (81%) than among individuals (16%) and between populations (3%). Evanno’s method shows that the likely number of sub-populations is 2 as influenced by the agroecological zone while Structure showed admixture between the two populationsdespite the low observed inbreeding. These results suggest a weak structuring of the CAR native chicken population and great possibilities for selection and genetic improvement. However, SSR markers are neutral and further studies need to be done using functional markers to detect functional and productivity genes relevant to disease resistance, environmental resilience and production traits. En République Centrafricaine (RCA), la production avicole repose principalement sur la poule locale dite indigène (Gallus gallus domesticus). Cette ressource n’a jamais été génétiquement caractérisée malgré l’énorme potentiel économique découlant de son exploitation en milieu rural et périurbain. Cette étude avait pour but d’évaluer la diversité génétique de la poule locale en RCA par génotypage à l’aide de 16 marqueurs microsatellites. Des échantillons de sang ont été prélevés au hasard sur 205 sujets adultes provenant de deux des quatre zones agroécologiques de RCA, dont 102 en zone forestière et 103 en savane. Les résultats ont révélé que 16 marqueurs microsatellites ont été amplifiés avec un taux d’amplification de 61,54 % des marqueurs recommandés pour l’espèce poule. La valeur moyenne du Fis a été faible et positive (0,16) suggérant une faible consanguinité et une faible réduction de l’hétérozygotie. La diversité génétique globale (0,54), l’hétérozygotie moyen (0,45) et la fréquence allélique élevée (0,61) ont confirmé une variabilité génétique modérée à élevée au sein de la population de poule locale de la RCA. La variance moléculaire au sein de l’individu a été très élevée (81 %) qu’entre individus (16 %) et entre populations (3 %). La méthode d’Evanno montre que le nombre probable de sous-populations est de 2, tandis que la structure génétique a confirmé un brassage de deux sous populations et une faible consanguinité observée. Ces résultats suggèrent une faible structuration de la population de poules originaires de RCA et une possibilité de sélection et d’amélioration génétique. Cependant, les microsatellites étant des marqueurs neutres, des études supplémentaires doivent être réalisées à l’aide des marqueurs fonctionnels pour détecter les gènes utiles en vue de l’amélioration des performances de production et d’adaptabilité .

Genetic matching and the identification of a promising biocontrol agent validates a decision to survey natural enemies of Urena lobata in Malaysia

Article

May 2024
BIOL CONTROL

Analysis of the genetic structure of populations of the terrestrial mollusk Caucasotachea vindobonensis (Helicidae) in conditions at the eastern border of the range using microsatellite markers

Article

Apr 2024

BACKGROUND: The aim of the study was to study the genetic structure of Caucasotachea vindobonensis populations in the south of the Central Russian Upland using SSR markers. MATERIALS AND METHODS Genetic structure of the populations was studied using eight microsatellite markers, first identified by the authors for the species under study. Fragment analysis of PCR products was carried out on an automatic capillary DNA sequencer Nanophore 05 (IAP RAS, Russia). A total of 498 individuals from 24 populations were studied. RESULTS: A total of 59 alleles were isolated in the eight studied STR loci, of which 21 (36%) turned out to be private. At the same time, private alleles were found in eleven studied populations, which is 46% of their total number. According to the data obtained, the effective number of alleles (Ae) averaged 1.6±0.06, the Chenon index (I) was 0.45±0.03, and the level of expected heterozygosity (He) was 0.27±0.021. A high level of spatial subdivision of population gene pools was noted (Fst=0.47±0.08) with a fairly low level of gene flow (Nm=1.15±0.91). PCA analysis showed that the populations of the central and eastern parts of the south of the Central Russian Upland form a closely related group, different from other populations of the region. Calculation of the effective abundance using the LD method showed that NeLd varies in different groups of snails from 0.6 to infinity. CONCLUSIONS: Populations of C. vindobonensis in the south of the Central Russian Upland live in conditions of significant isolation, as evidenced by the high degree of differentiation of the studied groups. The analysis of principal components based on genetic distances according to Nei and Wright's F-statistics indicate a pronounced division of populations in the study area into two clusters, which is probably associated with the historical features of landscape formation. Calculation of effective numbers indicates the high viability of the majority of the studied populations. At the same time, some groups of snails are clearly in a depressed state, which is reflected in low levels of genetic diversity and their effective size.

Revealing the genomic diversity of North-western Indian people through 20 hypervariable genetic markers

Article

May 2024

To explore the genetic diversity within the North-western Indian population, a sample of 216 individuals, selected at random to be representative, underwent genotyping using 20 highly variable autosomal STR markers. Through statistical analysis, it was determined that the Penta E locus displayed the highest degree of polymorphism (0.905) and discrimination (0.982), while the TH01 locus exhibited the lowest levels of polymorphism (0.647) and discrimination (0.855) among all the markers used. The Penta E locus also displayed the highest observed heterozygosity (0.884), while the D5S818 locus had the least observed heterozygosity (0.671) among all the markers. When comparing the studied population with others, it was found to be genetically closely related to the Rajasthani population. These findings have implications for population genetics, forensic applications, and medical research, particularly in the development of an optimal set of polymorphic STR markers for the North-western Indian population. The genomic data of this study will be served for the forensic and medical application.

Extra-pair paternity in the Wood Warbler (Phylloscopus sibilatrix) in Central Russia

Article

May 2024

Extra-pair paternity is widespread in passerine birds. The number of extra-pair young (EPY) varies among different species and populations of the same species. We tested if it is a case for a small passerine bird with poly-territorial behaviour, the Wood Warbler (Phylloscopus sibilatrix). The results are based on the microsatellite analysis of seven loci and revealed a high level of EPY in Central Russia population of Wood Warbler (EPY in 41% of all nests, 16 of 39 nests; 25% of all young were EPY, 52 of 212 young). We did not find relationship between relatedness among mates in the pair and the presence of EPY. There was no difference in heterozygosity and body mass between EPY and within pair young (WPY). Possible causes of extra-pair paternity are discussed.

Proximal Causes of Natal Dispersal in Belding's Ground Squirrels (Spermophilus Beldingi)

Article

Full-text available

Dec 1986

Kay E Holekamp

I studied the proximal factors influencing dispersal from the natal site in two free-living populations of Belding's ground squirrels (Spermophilus beldingi) in the Sierra Nevada of California. I tested 10 hypotheses, each suggesting a different social, ecological, or ontogenetic factor as a proximal cause of natal dispersal in this species. Using discriminant analysis I also examined effects on dispersal of several independent variables concurrently. Data from marking and live-trapping studies over three field seasons (1979-1981) failed to support hypotheses suggesting resource shortage, ectoparasite load, social facilitation, conspecific aggression, or avoidance by conspecifics as proximal causes of natal dispersal in S. beldingi. Furthermore, dispersal is apparently not caused by changes in juveniles' response thresholds to conspecific aggression or by juveniles' attempts to avoid members of their family units, nearest neighbors, or other members of their local populations. My data supported an @'ontogenetic switch@' hypothesis that suggests natal dispersal by male S. beldingi is triggered by attainment of a particular body mass or body composition, or some combination of these two variables. Other data indicated that this ontogenetic switch initiates not only dispersal behavior per se, but also a larger syndrome o behaviors that appear to be functionally related to dispersal. Specifically, this syndrome involves changes in exploration, responses to frightening stimuli, and locomotor behavior exhibited by dispersers. I discuss possible relationships among variables operating at different proximal levels (sensu Tinbergen) to cause natal dispersal in S. beldingi and other mammals. I conclude that a complex suite of variables probably operates at genetic, physiological, and socioecological levels to proximally cause natal dispersal in each species. The ultimate (evolutionary) hypotheses most consistent with my data from S. beldingi are that dispersal: (1) reduces nuclear family incest, (2) optimizes inbreeding, and (3) improves access to mates.

Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data

Article

Full-text available

Jul 1992

We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

Microsatellite analysis of population-structure in Canadian Polar Bears

Article

Full-text available

Jul 1995

Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait-Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long-distance seasonal movements undertaken by polar bears.

Estimation of Pairwise Relatedness With Molecular Markers

Article

Full-text available

Sep 1999

Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears.

Paetkau D, Slade R, Burden M, Estoup A. Direct, real-time estimation of migration rate using assignment methods: a simulation-based exploration of accuracy and power. Mol Ecol 13: 55-65

Article

Full-text available

Feb 2004

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.

Introduction to Conservation Genetics

Book

Mar 2002

The biological diversity of our planet is being depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding depression an inevitable consequence for many species. This textbook provides a clear and comprehensive introduction to the importance of genetic studies in conservation. The text is presented in an easy-to-follow format with main points and terms clearly highlighted. Each chapter concludes with a concise summary, which, together with worked examples and problems and answers, emphasise the key principles covered. Text boxes containing interesting case studies and other additional information enrich the content throughout, and over 100 beautiful pen and ink portraits of endangered species help bring the material to life.

Article

Mar 1989
EVOLUTION

A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.

Two-generation analysis of pollen flow across a landscape I. Male gamete heterogeneity among females

Article

Feb 2001

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processess and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model's elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model's effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by ΦFT, a male gametic analogue of Wright's FST and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that ΦFT= 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

Article

Mar 1989

Mark–recapture by genetic tagging reveals restricted movements by bush rats (Rattus fuscipes) in a fragmented landscape

Article

Dec 2005
J ZOOL

We applied genetic tagging (the identification of individuals by genetic markers) as part of a demographic and genetic analysis of a manipulative study of bush rats Rattus fuscipes in a fragmented landscape in south-eastern Australia. Our study comprised bush rat populations from 30 remnant patches embedded within an extensive exotic pine plantation. Genetic tagging was applied at 12 sites where eight or more animals were encountered in the initial census. Out of a total of 701 DNA samples, we determined (by genetic analysis at 11 microsatellite loci) that 588 bush rat individuals were sampled. Genetic tagging proved to be highly effective, with 97% of animals uniquely identified with three loci, and all animals identified by six loci. Mark–recapture distances moved by genetically tagged animals from the control sites and post-perturbation treatment samples were highly restricted, with a mean of 35 m (35.3±4.5, mean±se, max. 280 m, n=109). This mean distance moved appears to be lower than for other comparable studies of the species. Fragmentation and above-average densities of animals may partially explain this result. An analysis of the factors affecting mark–recapture distance indicated that there was a significant effect of trap layout on the maximum movement detected, but no significant difference in mark–recapture distance between the sexes. We have demonstrated that genetic tagging can facilitate traditional capture–mark–recapture studies in bush rats and pave the way for subsequent population genetic analyses that can offer additional insights not available from ecology alone.

Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloë dactyloides

Article

Apr 1995
MOL ECOL

Buffalograss, Buchloë dactyloides, is widely distributed throughout the Great Plains of North America, where it is an important species for rangeland forage and soil conservation. The species consists of two widespread polyploid races, with narrowly endemic diploid populations known from two regions: central Mexico and Gulf Coast Texas. We describe and compare the patterns of allozyme and RAPD variation in the two diploid races, using a set of 48 individuals from Texas and Mexico (four population samples of 12 individuals each). Twelve of 22 allozyme loci were polymorphic, exhibiting 35 alleles, while seven 10-mer RAPD primers revealed 98 polymorphic bands. Strong regional differences were detected in the extent of allozyme polymorphism: Mexican populations exhibited more internal gene diversity (He= 0.20, 0.19) than did the Texan populations (He= 0.08, 0.06), although the number of RAPD bands in Texas (n= 62) was only marginally smaller than in Mexico (n= 68). F-statistics for the allozyme data, averaged over loci, revealed strong regional differentiation (mean FRT=+ 0.30), as well as some differentiation among populations within regions (mean FPR=+ 0.09). In order to describe and compare the partitioning of genetic variation for multiple allozyme and RAPD loci, we performed an Analysis of Molecular Variance (AMOVA). AMOVA for both allozyme and RAPD data revealed similar qualitative patterns: large regional differences and smaller (but significant) population differences within regions. RAPDs revealed greater variation among regions (58.4% of total variance) than allozymes (45.2%), but less variation among individuals within populations (31.9% for RAPDs vs. 45.2% for allozymes); the proportion of genetic variance among populations within regions was similar (9.7% for RAPDs vs. 9.6% for allozymes). Despite this large-scale concordance of allozyme and RAPD variation patterns, multiple correlation Mantel techniques revealed that the correlations were low on an individual by individual basis. Our findings of strong regional differences among the diploid races will facilitate further study of polyploid evolution in buffalograss.

Estimators for pairwise relatedness and individual inbreeding coefficients

Article

Apr 1996
GENET RES

Kermit Ritland

Method-of-moments estimators (MMEs) for the two-gene coefficients of relationship and inbreeding, and for thxe four-gene Cotterman coefficients, are described. These estimators, which use co-dominant genetic markers, are most appropriate for estimating pairwise relatedness or individual inbreeding coefficients, as opposed to their mean values in a group. This is because, compared to the maximum likelihood estimate (MLE), they show reduced small-sample bias and lack distributional assumptions. The ‘efficient’ MME is an optimally weighted average of estimates given by each allele at each locus. Generally, weights must be computed numerically, but if true coefficients are assumed zero, simplifiedestimators are obtained whose relative efficiencies are quite high. Population gene frequency is assumed to be assayed ina larger, ‘reference population’ sample, and the biases introduced by small reference samples and/or genetic drift of the reference population are discussed. Individual-level estimates of relatedness or inbreeding, while displaying high variance, are useful in several applications as a covariate in population studies.

Multiple Regression and Correlation Extensions of the Mantel Test of Matrix Correspondence

Article

Dec 1986
Syst Zool

Principles Of Population Genetics

Article

Jun 1990

Do harvest refuges buffer kangaroos against evolutionary responses to selective harvesting?

Article

Jul 2004

There is a wealth of literature documenting a directional change of body size in heavily harvested populations. Most of this work concentrates on aquatic systems, but terrestrial populations are equally at risk. This paper explores the capacity of harvest refuges to counteract potential effects of size-selective harvesting on the allele frequency,of populations. We constructed a stochastic, individual-based model parameterized with data on red kangaroos. Because we do not know which part of individual growth would change in the course of natural selection, we explored the effects of two alternative models of individual growth in which alleles affect either the growth rate or the maximum size. The model results show that size-selective harvesting can result in significantly smaller kangaroos for a given age when the entire population is subject to harvesting. In contrast, in scenarios that include dispersal from harvest refuges, the initial allele frequency remains virtually unchanged.

Genetics Of Populations

Article

Jan 2000

P.W. Hedrick

Smouse PE, Peakall R. Spatial autocorrelation analysis of multi-allele and multi-locus genetic microstructure. Heredity 82: 561-573

Article

Jun 1999
HEREDITY

Population genetic theory predicts that plant populations will exhibit internal spatial autocorrelation when propagule flow is restricted, but as an empirical reality, spatial structure is rarely consistent across loci or sites, and is generally weak. A lack of sensitivity in the statistical procedures may explain the discrepancy. Most work to date, based on allozymes, has involved pattern analysis for individual alleles, but new PCR-based genetic markers are coming into vogue, with vastly increased numbers of alleles. The field is badly in need of an explicitly multivariate approach to autocorrelation analysis, and our purpose here is to introduce a new approach that is applicable to multiallelic codominant, multilocus arrays. The procedure treats the genetic data set as a whole, strengthening the spatial signal and reducing the stochastic (allele-to-allele, and locus-to-locus) noise. We (i) develop a very general multivariate method, based on genetic distance methods, (ii) illustrate it for multiallelic codominant loci, and (iii) provide nonparametric permutational testing procedures for the full correlogram. We illustrate the new method with an example data set from the orchid Caladenia tentaculata, for which we show (iv) how the multivariate treatment compares with the single-allele treatment, (v) that intermediate frequency alleles from highly polymorphic loci perform well and rare alleles poorly, (vi) that a multilocus treatment provides clearer answers than separate single-locus treatments, and (vii) that weighting alleles differentially improves our resolution minimally. The results, though specific to Caladenia, offer encouragement for wider application.

Genetic detection of sex-biased dispersal

Article

Jul 1999

We investigated the application of a recently developed genetic test for sex bias in dispersal. This test determines an animal's 'assignment index' or the expected frequency of its genotype in the population in which it is captured. Low assignment indices indicate a low probability of being born locally. We investigated the use of this test with the white-footed mouse, Peromyscus leucopus, in which dispersal is predominantly male-biased, but not extreme. We found that male P. leucopus had significantly lower assignment indices than females. These data suggest that the genetic test for sex bias in dispersal has potential to be used with species that do not have extreme sex-biased dispersal tendencies.

Two-generation analysis of pollen flow across a landscape. I. Male gamete heterogeneity among females

Article

Mar 2001

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processess and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model's elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model's effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by phiFT, a male gametic analogue of Wright's F(ST) and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that phiFT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

Y chromosome conserved anchored tagged sequences (YCATS) for the analysis of mammalian male-specific DNA

Article

Feb 2003

Y chromosome haplotyping based on microsatellites or single nucleotide polymorphisms has recently proven to be a powerful approach for evolutionary studies of human populations, and also holds great promise for the studies of wild species. However, the use of the approach is hampered in most natural populations by the lack of Y chromosome markers and sequence information. Here, we report the large-scale development of Y chromosome conserved anchor tagged sequence (YCATS) markers in mammals by a polymerase chain reaction screening approach. Exonic primers flanking 48 different introns of Y-linked genes were developed based on human and mouse sequences, and screened on a set of 20 different mammals. On average about 10 introns were amplified for each species and a total of 100 kb of Y chromosome sequence were obtained. Intron size in humans was a reasonable predictor of intron size in other mammals (r2 = 0.45) and there was a negative correlation between human fragment size and amplification success. We discuss a number of factors affecting the possibility of developing conserved Y chromosome markers, including fast evolution of Y chromosome sequences due to male-biased mutation and adaptive evolution of male-specific genes, dynamic evolution of the Y chromosome due to being a nonrecombining unit, and homology with X chromosome sequences.

Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat, Rattus fuscipes

Article

May 2003

Dispersal is a fundamental process that influences the response of species to landscape change and habitat fragmentation. In an attempt to better understand dispersal in the Australian bush rat, Rattus fuscipes, we have combined a new multilocus autocorrelation method with hypervariable microsatellite genetic markers to investigate fine-scale (< or = 1 km) patterns of spatial distribution and spatial genetic structure. The study was conducted across eight trapping transects at four sites, with a total of 270 animals sampled. Spatial autocorrelation analysis of bush rat distribution revealed that, in general, animals occurred in groups or clusters of higher density (< or = 200 m across), with intervening gaps or lower density areas. Spatial genetic autocorrelation analysis, based on seven hypervariable microsatellite loci (He = 0.8) with a total of 80 alleles, revealed a consistent pattern of significant positive local genetic structure. This genetic pattern was consistent for all transects, and for adults and sub-adults, males and females. By testing for autocorrelation at multiple scales from 10 to 800 m we found that the extent of detectable positive spatial genetic structure exceeded 500 m. Further analyses detected significantly weaker spatial genetic structure in males compared with females, but no significant differences were detected between adults and sub adults. Results from Mantel tests and hierarchical AMOVA further support the conclusion that the distribution of bush rat genotypes is not random at the scale of our study. Instead, proximate bush rats are more genetically alike than more distant animals. We conclude that in bush rats, gene flow per generation is sufficiently restricted to generate the strong positive signal of local spatial genetic structure. Although our results are consistent with field data on animal movement, including the reported tendency for males to move further than females, we provide the first evidence for restricted gene flow in bush rats. Our study appears to be the first microsatellite-based study of fine-scale genetic variation in small mammals and the first to report consistent positive local genetic structure across sites, age-classes, and sexes. The combination of new forms of autocorrelation analyses, hypervariable genetic markers and fine-scale analysis (< 1 km) may thus offer new evolutionary insights that are overlooked by more traditional larger scaled (> 10 km) population genetic studies.

Dispersal, philopatry, and infidelity: Dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus)

Article

Apr 2005

Dispersal influences evolution, demography, and social characteristics but is generally difficult to study. Here we combine long-term demographic data from an intensively studied population of superb fairy-wrens (Malurus cyaneus) and multivariate spatial autocorrelation analyses of microsatellite genotypes to describe dispersal behavior in this species. The demographic data revealed: (1) sex-biased dispersal: almost all individuals that dispersed into the study area over an eight-year period were female (93%; n = 153); (2) high rates of extragroup infidelity (66% of offspring), which also facilitated local gene dispersal; and (3) skewed lifetime reproductive success in both males and females. These data led to three expectations concerning the patterns of fine-scale genetic structure: (1) little or no spatial genetic autocorrelation among females, (2) positive spatial genetic autocorrelation among males, and (3) a heterogeneous genetic landscape. Global autocorrelation analysis of the genotypes present in the study population confirmed the first two expectations. A novel two-dimensional local autocorrelation analysis confirmed the third and provided new insight into the patterns of genetic structure across the two-dimensional landscape. We highlight the potential of autocorrelation analysis to infer evolutionary processes but also emphasize that genetic patterns in space cannot be fully understood without an appropriate and intensive sampling regime and detailed knowledge of the individuals genotyped.

Genetic Analysis in Excel. The Australian National University Introduction to Con-servation Genetics Principles of Population Genetics Genetics of Populations Estimation of pairwise relatedness with molecular markers

Jan 1997
1753-1766

Flanagan
R Frankham
Jd Ballou
Briscoe
Da

Flanagan NS (2005) A Guide to GENALEX 6. Genetic Analysis in Excel. The Australian National University, Canberra, Australia http://www.anu.edu.au/BoZo/GenAlEx/. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Con-servation Genetics. Cambridge University Press, Cambridge. Hartl DL, Clark AG (1997) Principles of Population Genetics, 3rd edn. Sinauer Associates Inc., Sunderland, MA. Hedrick PW (2000) Genetics of Populations, 2nd edn. Jones and Bartlett, Boston. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics, 152, 1753 – 1766.

A Primer of Ecological Genetics

Con Ner JK
Hartl DL

A Guide to genalex 6. Genetic Analysis in Excel

Flanagan NS

Jan 2002

Frankham R

GENALEX 6: Genetic Analysis in Excel. Population genetic software for teaching and research

Abstract

No full-text available

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