New technological methods, such as rapidly developing molecular approaches, often provide new tools for scientific advances. However, these new tools are often not utilized equally across different research areas, possibly leading to disparities in progress between these areas. Here, we use empirical evidence from the scientific literature to test for potential discrepancies in the use of genetic tools to study parasitic vs non-parasitic organisms across three distinguishable molecular periods, the allozyme, nucleotide and genomics periods. Publications on parasites constitute only a fraction (<5%) of the total research output across all molecular periods and are dominated by medically relevant parasites (especially protists), particularly during the early phase of each period. Our analysis suggests an increasing complexity of topics and research questions being addressed with the development of more sophisticated molecular tools, with the research focus between the periods shifting from predominantly species discovery to broader theory-focused questions. We conclude that both new and older molecular methods offer powerful tools for research on parasites, including their diverse roles in ecosystems and their relevance as human pathogens. While older methods, such as barcoding approaches, will continue to feature in the molecular toolbox of parasitologists for years to come, we encourage parasitologists to be more responsive to new approaches that provide the tools to address broader questions.

Technological advances in molecular biology have contributed substantially to our understanding of plant genetic diversity. Early studies of allozyme variation employing protein electrophoresis revealed that plant populations have high levels of genetic diversity, most of the variation at polymorphic loci is found within populations, and geographic range and breeding system explain the largest proportion of variation in genetic diversity. With the discovery of restriction endonucleases, the first DNA-based markers allowed the detection of variation in DNA sequences in plant population studies. More recently, techniques that utilize the polymerase chain reaction have allowed a more representative assessment of genetic variation in plants by screening multiple loci distributed throughout the genome. The analyses reveal sufficient polymorphism for the examination of fine-scale genetic differences among individuals. Information on plant genetic diversity is also emerging from studies of plant genome structure. Comparative genetic mapping studies of members of the Brassicaceae, Poaceae, and Solanaceae show that gene content is highly conserved between closely related species, although gene order on a chromosomal segment may differ between species. Comparative sequencing studies reveal higher degrees of diversity at the microstructural (less than 1 million base pairs) level than predicted at the genetic map level and suggest that genes are densely packed in gene-rich regions, rather than randomly distributed along chromosomes in species with large genomes. Sequencing of the entire genomes of rice and Arabidopsis thaliana will help identify genes controlling agronomically important traits, improve our understanding of genetic variation for fitness-related traits in wild plant populations including weed species, resolve evolutionary relationships among plant taxa, and potentially revolutionize current ideas on plant diversity and evolution.

Eight taxa have recently been proposed as being encompassed by the genus Trichinella on the basis of allozyme and biological data. In this paper we show that an analogous 8 taxon structure for this genus results from the random amplified polymorphic DNAs (RAPDs). Five 10-mer or 20-mer primers were used under different polymerase chain reaction (PCR) conditions to produce multiband RAPD fingerprints from muscle larvae of 40 isolates of Trichinella spp. The resulting RAPD data were analysed following the numerical taxonomic approach, and the resulting classification was compared to that derived from allozyme data. The agreement found between allozymes and RAPDs, while supporting the polyspecific structure of the genus Trichinella, confirms the potential of RAPDs as a tool for the detection of cryptic species. The selected primers were tested on individual muscle larvae in an attempt to standardize a RAPD assay for the routine identification of the 8 taxa of Trichinella. Only 1 of the 5 primers yielded reproducible fingerprints from the single larvae. Using this primer, the 5 species and the 3 other taxa of the genus Trichinella can be identified in a single assay without the need for massive in vivo parasite production.

Species of Protopolystoma are monogenean flukes that only infect allopolyploid hosts in the anuran genus Xenopus. Multivariate analyses of morphometric sclerite characters in the nominal species Protopolystoma simplicis suggest that morphologically distinguishable populations occur in the tetraploid host, Xenopus laevis victorianus, and in each of the octoploid hosts, X. vestitus and X. wittei. The species-level divergence of a lineage specific to X. laevis is supported by sequence variation in the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Protopolystoma simplicis from X. laevis is redesignated P. microsclera n. sp., with P. simplicis being retained for populations in octoploid hosts. This division is consistent with large differences in egg hatching schedule, fixed differences at the mannose-6-phosphate isomerase and fumarate hydratase loci, and host-specificity in experimental analyses. Although the respective P. simplicis populations in X. vestitus and X. wittei also show significant diversity in allozyme expression, morphometrics and egg hatching schedule, they are retained in the same species because their level of mitochondrial DNA divergence is similar to that found within other Protopolystoma species. The consequences of splitting P. simplicis for a recent interpretation of the origin of Protopolystoma faunas in octoploid Xenopus spp. is discussed.

Genetic variation among 14 populations of Plutella xylostella (Linnaeus) from USA (Geneva, New York), Brazil (Brasilia), Japan (Okayama), The Philippines (Caragan de Oyo), Uzbekistan (Tashkent), France (Montpellier), Benin (Cotonou), South Africa (Johannesburg), Réunion Island (Montvert), and five localities in Australia (Adelaide, Brisbane, Mareeba, Melbourne, Sydney) were assessed by analysis of allozyme frequencies at seven polymorphic loci. Most of the populations were not in Hardy–Weinberg equilibrium and had a deficit in heterozygotes. The global differentiation among populations was estimated by the fixation index (Fst) at 0.103 for the 14 populations and at 0.047 when populations from Australia and Japan, which differed most and had a strong genetic structure, were excluded from the analysis. By contrast, the populations from Benin (West Africa) and Brazil (South America) were very similar to each other. Genetic differentiation among the populations was not correlated with geographical distance.

Tilapia species are able to hybridize in captivity or in natural conditions following introduction of alien species. Here, we report a case of hybridization between two (and perhaps three) autochthonous species, Tilapia zillii and T. guineensis, resulting from a modification of their environment due to human activities. The man-made dam Ayamé (Côte d'Ivoire) transformed the River Bia into a lake (Lake Ayamé, area: 197 km2). In this new environment, both tilapia species have hybridized. In order to study hybridization along the Bia System, 25 allozyme loci have been screened in 470 specimens from ten locations. Two loci LDH-1 and PGI-2 were diagnostic between the two different species and can be used to identify hybrids in each sampling location of the River Bia basin. The percentage of pure T. zillii individuals in Lake Ayamé varied from 18.1% in Ebikro to 4.2% in Kétesso while percentage of pure T. guineensis varied from 81.3% in Yaou to 50.0% in Ebikro. The proportions of hybrids varied from 8.3% in Yaou to 31.9% in Ebikro. The existence of private alleles observed in tilapia from Lake Ayamé compared to what has been observed in both reference populations, T. zillii and T. guineensis led to the hypothesis that a third species could have been engaged in this hybridization. This third species is likely to be T. busumana, formerly present in the lake but now rarely observed. If this natural hybridization is due to the dam construction and the correlated ecological changes, then other hybridizations could result since many dams have been constructed within the range of these species in Côte d'Ivoire.

Allozyme differentiation was investigated at 23 putative enzyme coding loci in 16 ommastrephid squids to identify species and to assess genetic relationships. The species examined were Illex illecebrosus, I. coindetii, I. argentinus, Todaropsis eblanae, Todarodes sagittatus, T. angolensis, T. filippovae, T. pacificus pacificus, Nototodarus sloanii, N. gouldi, Martialia hyadesi, Ommastrephes bartramii, Sthenoteuthis pteropus, S. oualaniensis, Eucleoteuthis luminosa, and Dosidicus gigas. A dendrogram based on Nei's genetic distance between the species closely approximates to the latest systematics based on morphological characters, but the positions of M. hyadesi and T. eblanae were considerably distant from all other species. The results demonstrate the benefits of further biochemical analysis to an understanding of the systematics of the ommastrephid squids.

Genetic diversity in four populations of the Eurasian badger Meles meles from Denmark was estimated by allozyme electrophoresis. Low genetic variability was found within populations as compared to the variability found in badger populations from other countries, whereas significant genetic differentiation was found between populations. The low genetic variability and the differentiation between populations is explained by the fragmentation of the Danish landscape, which reduces the effective population size of local populations and the gene flow between them. Low genetic variability found for Danish badgers also supports the hypothesis of a rapid recolonization following the last glaciation.

Starch gel electrophoresis was used to compare eight loci in six enzymatic systems of 17 samples of the groundnut seed-beetle, Caryedon serratus (Ol.) (Coleoptera: Bruchidae) bred on five different host-plant species: Arachis hypogaea, Bauhinia rufescens, Cassia sieberiana, Piliostigma reticulatum and Tamarindus indica. The rate of polymorphism was 44.8%. The average genetic diversity (Hw) was 0.184. Allozyme variability analysis indicated that seed-beetles associated with P. reticulatum and groundnut, Arachis hypogaea were genetically similar, whereas other samples clustered according to their host plant species. Geographical distances less than 400 km were not decisive for the genetic structuring of samples associated with a given host plant.