Comparative Analysis of Phylogenetic Relationships of Grain Amaranths and Their Wild Relatives (Amaranthus; Amaranthaceae) Using Internal Transcribed Spacer, Amplified Fragment Length Polymorphism, and Double-Primer Fluorescent Intersimple Sequence Repeat Markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

Low-Cot DNA sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus

We examined genetic diversity and relationships among 24 cultivated and wild Amaranthus accessions using the total low-Cot DNA and five individual repetitive sequences as probes. These low-Cot DNA probes were obtained by the isolation of various classes of repetitive-DNA sequences, including satellites, minisatellites, microsatellites, rDNA, retrotransposon-like sequences, and other unidentified novel repetitive sequences. DNA fingerprints generated by different types of repetitive-DNA probes revealed different levels of polymorphism in the Amaranthus genomes. A repetitive sequence containing microsatellites was found to be a suitable probe for characterizing intraspecific accessions, whereas more conservative sequences (e.g. rDNA) were informative for resolving phylogenetic relationships among distantly related species.Genetic diversity, measured as restriction fragment length polymorphism (RFLP) and the similarity index at the low-Cot DNA level, was equally high among intraspecific accessions between the two species groups: grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus) and their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis). At the interspecific level, however, the grain amaranth species are less divergent from each other than their wild progenitors. With the rare exceptions of certain A. caudatus accessions, grain amaranths were found to be closely related to A. hybridus. The results based on low-Cot DNA were comparable with previous RAPD and isozyme studies of the same set of species/accessions of Amaranthus, indicating that low-Cot DNA sequences are suitable probes for a fingerprinting analysis of plant germplasm diversity and for determining phylogenetic relationships. Received: 19 October 1998 / Accepted: 8 January 1999     

Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus

 Genetic diversity and relationships of 23 cultivated and wild Amaranthus species were examined using both isozyme and RAPD markers. A total of 30 loci encoding 15 enzymes were resolved, and all were polymorphic at the interspecific level. High levels of inter-accessional genetic diversity were found within species, but genetic uniformity was observed within most accessions. In the cultivated grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus), the mean value of H_T was 0.094, H_S was 0.003, and G_ST was 0.977 at the species level. The corresponding values in their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis) were 0.135, 0.004, and 0.963, respectively. More than 600 RAPD fragments were generated with 27 arbitrary 10-base primers. On average, 39.9% of the RAPD fragments were polymorphic among accessions within each crop species; a similar level of polymorphism (42.8%) was present in the putative progenitors, but much higher levels of polymorphism were found in vegetable (51%) and other wild species (69.5%). The evolutionary relationships between grain amaranths and their putative ancestors were investigated, and both the RAPD and isozyme data sets supported a monophyletic origin of grain amaranths, with A. hybridus as the common ancestor. A complementary approach using information from both isozymes and RAPDs was shown to generate more accurate estimates of genetic diversity, and of relationships within and among crop species and their wild relatives, than either data set alone. Received: 13 March 1997/Accepted: 6 May 1997     

Genome analysis of amaranths: Determination of inter- and intra-species variations

Amaranths are an important group of plants and include grain, vegetable and ornamental types. Despite the economic importance of the amaranths, there is very little information available about the extent and nature of genetic diversity present in the genus Amaranthus at molecular level. We now report the randomly amplified polymorphic DNA (RAPD) profiles of different species of Amaranthus as well as different accessions of the species. These RAPD analyses have been carried out using 65 arbitrary sequence decamer primers. From the RAPD data, an UPGMA dendrogram illustrating the inter-as well as intra-species relationships has been computed. The putative hybrid origin of A.dubious from A. hybridus and A. spinosus is also ruled out by the RAPD data. The trends of species relationships amongst the amaranths determined by RAPDs is consistent with their cytogenetic and evolutionary relationships that have already been determined. NBRI Communication No:464 (N.S.).     

赖草属植物的分类现状及主要存在的问题

赖草属(Leymus Hochst.)为禾本科(Poaceae)小麦族(Triticeae)中的一个有重要经济价值的属,属内多数种类是优良牧草,有些种类具有耐寒、耐旱、耐碱等特性,是农业良种繁育、畜牧业牧草改良利用的重要基因资源。该属在分类学上是一个疑难属,在属的界限、属下组系的划分,以及类群间演化关系上问题较多。对赖草属分类学问题进行了综述,为赖草属植物资源的开发利用和保护提供资料。     

Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers.

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

Beyond landraces: developing improved germplasm resources for underutilized species – a case for Bambara groundnut

The potential for underutilized crops (also known as minor, neglected or orphan crops) to improve food and nutrition security has been gaining prominence within the research community in recent years. This is due to their significance for diversified agricultural systems which is a necessary component of future agriculture to address food and nutritional security concerns posed by changing climate and a growing world population. Developing workable value chain systems for underutilized crop species, coupled with comparative trait studies with major crops, potentially allows us to identify suitable agricultural modalities for such species. Bambara groundnut (Vigna subterranea L. Verdc.), an underutilized leguminous species, is of interest for its reported high levels of drought tolerance in particular, which contributes to environmental resilience in semi-arid environments. Here, we present a synopsis of suitable strategies for the genetic improvement of Bambara groundnut as a guide to other underutilized crop species. Underutilized crops have often been adapted over thousands of years in particular regions by farmers and largely still exist as landraces with little or no genetic knowledge of key phenotypic traits. Breeding in these species is fundamentally different to breeding in major crops, where significant pedigree structures and history allow highly directed improvement. In this regard, deploying new integrated germplasm development approaches for variety development and genetic analysis, such as multi-parent advance generation inter-crosses (MAGIC), within breeding programmes of underutilized species will be important to be able to fully utilize such crops.     

Strong correlation between cross-amplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci

The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species.     

Systematics and phylogeography of Acanthodactylus schreiberi and its relationships with Acanthodactylus boskianus (Reptilia: Squamata: Lacertidae)

Acanthodactylus is a widespread lacertid genus occurring from the Iberian Peninsula and western North Africa to western India including the Middle East, Cyprus, and the Arabian Peninsula. The genus is in dire need of a taxonomic revision, and the phylogenetic relationships amongst and within its species remain unclear. In particular, the taxonomy and relationship of the allopatric, narrow‐ranged Acanthodactylus schreiberi and its close relative, the widespread Acanthodactylus boskianus asper, are poorly understood. We estimated the phylogenetic and phylogeographical structure of A. schreiberi across its distribution range, and evaluated its relationships to A. b. asper, using mitochondrial and nuclear data. The phylogenetic results indicate that both species are paraphyletic, with A. schreiberi nested within A. b. asper, and the subspecies A. schreiberi syriacus nested within a distinct lineage of A. b. asper. We suggest that the group is in need of a taxonomic revision because the identified lineages and genetic diversity are incongruent with the currently recognized taxonomy. We tentatively conclude that A. schreiberi is restricted to Cyprus and Turkey, reduced to a single form, and that the populations in Lebanon and Israel belong to A. b. asper. © 2014 The Linnean Society of London     

Plitvice Lakes National park harbors ancient,yet endangered diversity of trout (genus Salmo)

National park Plitvice Lakes is the oldest, the largest and the most visited national park in Croatia, well known for its stunning karstic watersheds that supply Plitvice Lakes and exceptionally valuable biodiversity. Lack of knowledge on the taxonomic status, population structure and viability of trout in the Plitvice Lakes National park, as well as the possibility of existence of cryptic diversity, motivated this study which aimed to determine: taxonomic status and phylogenetic relationship of Plitvice Lakes trout with other Salmo species, genetic structure and diversity of their populations, as well as future viability of populations. 150 samples of trout were obtained from 17 localities. Two mitochondrial gene markers, gene for cytochrome b and mitochondrial control region were used in phylogenetic reconstruction, as well as in population genetic investigation. Intraspecific and intrapopulation genetic diversity was described by calculating several measures of genetic polymorphism, while gene flow among populations was estimated as the migration rates and as the number of immigrants per generation. Phylogenetic trees revealed that Plitvice Lakes watershed is inhabited by two evolutionary independent units of the genus Salmo, representing two species, Salmo labrax Pallas, 1814 and Salmo trutta Linnaeus, 1758. Possibly ‘pure’ populations of both species were found alongside several admixed ones in which both species are present. Our data has shown low intraspecific and intrapopulational diversities for Plitvice Lakes trout and restricted gene flow. Small effective sizes of populations and weak interconnections between them, which are most likely a consequence of fragmentation and habitat degradation, accentuating the need for urgent conservation measures.     

Pollen morphology of Chamaebuxus (DC.) Schb., Chodatia Paiva and Rhinotropis (Blake) Paiva (Polygala L., Polygalaceae)

Polygala L. is a large and highly diverse genus with complex taxonomy, but pollen morphological information for this taxon is scarce. In the present study, pollen characters have been used to assess the taxonomic delimitation and phylogenetic relationships of three newly established subgenera of Polygala: Chamaebuxus, Chodatia and Rhinotropis (sensu Paiva). The pollen morphology of 22 species has been examined using light microscopy and scanning electron microscopy of acetolysed material. The pollen of 15 of the species is examined for the first time. The pollen grains are isopolar, radially symmetrical, tectate and, typically, polyzonocolporate with numerous colpi running parallel to the polar axis, and an endocingulum around the equator. Two pollen types can be distinguished: Type I, which includes species belonging to Rhinotropis, and Type II, which includes species from Chamaebuxus and Chodatia. The two pollen types are described and the pollen of the three studied subgenera is illustrated. Despite the low infrageneric morphological diversity observed within the genus Polygala, quantitative characters of pollen grains support the current classification of the subgenera Chamaebuxus, Chodatia and Rhinotropis, and reveal a closer relationship between the first two taxa. Pollen characters are shown to be a useful and informative tool for assessing taxonomic position and phylogenetic relationships within Polygalaceae, especially at higher taxonomic levels.     

Genetic and Electron-Microscopic Characterization of ‘<Emphasis Type="Italic">Rickettsiella agriotidis</Emphasis>’, a new <Emphasis Type="Italic">Rickettsiella</Emphasis> Pathotype Associated with Wireworm, <Emphasis Type="Italic">Agriotes</Emphasis> sp. (Coleoptera: Elateridae)

Wireworms, the polyphagous larvae of click beetles belonging to the genus Agriotes (Coleoptera: Elateridae), are severe and widespread agricultural pests affecting numerous crops. A previously unknown intracellular bacterium has been identified in a diseased Agriotes larva. Microscopic studies revealed the subcellular structures characteristic of Rickettsiella infections. Molecular phylogenetic analysis based on 16S ribosomal RNA and signal recognition particle receptor (FtsY) encoding sequences demonstrates that the wireworm pathogen belongs to the taxonomic genus Rickettsiella. Therefore, the new pathotype designation ‘R. agriotidis’ is proposed to refer to this organism. Moreover, genetic analysis makes it likely that—on the basis of the currently accepted organization of the genus Rickettsiella—this new pathotype should be considered a synonym of the nomenclatural type species, Rickettsiella popilliae.     

Monophyletic clades of Macaranga‐pollinating thrips show high specificity to taxonomic sections of host plants

Thrips (Thysanoptera) have been recorded as pollinators of various plant species, but they are mostly regarded to be of low ecological relevance. In Southeast Asia, thrips were recently discovered to pollinate flowers of several taxonomic sections of the pioneer tree genus Macaranga (Euphorbiaceae), which is particularly well known as an ant‐plant, and for its importance in early forest succession. The lack of taxonomic treatment and of knowledge about systematic relationships among extant thrips, however, has prevented firm conclusions on the specificity of this plant–pollinator interaction. Here, results from sequencing of the mitochondrial cytochrome oxidase subunit support our previous morphospecies concept of Macaranga flower thrips, and confirm the genetic identity of five recently described species. They were remarkably all assigned to the genus Dolichothrips (Phlaeothripidae), which typically consists of phytophagous species. In addition, the molecular data revealed one cryptic species. A first phylogenetic tree of the Dolichothrips associated with Macaranga provides insights into their systematic position. In particular, we identify monophyly of all important Macaranga pollinator species, all species being largely specific to particular taxonomic host plant sections. Our results suggest a closely matched diversification of pollinating thrips with Macaranga trees. This adds a novel type of association to thrips pollinator–plant interactions, which have been so far documented as single‐species interactions or generalist thrips species visiting multiple plant taxa.     

Diversity and evolution of African Grass Rats (Muridae: Arvicanthis)—From radiation in East Africa to repeated colonization of northwestern and southeastern savannas

African Grass Rats of the genus Arvicanthis Lesson, 1842, are one of the most important groups of rodents in sub‐Saharan Africa. They are abundant in a variety of open habitats, they are major agricultural pests, and they became a popular model in physiological research because of their diurnal activity. Despite this importance, information about their taxonomy and distribution is unsatisfactory, especially in eastern Africa. In this study, we collected the most comprehensive multilocus DNA dataset to date across the geographic and taxonomic range of the genus (229 genotyped specimens from 130 localities in 16 countries belonging to all currently recognized species). We reconstructed phylogenetic relationships, mapped the distribution of major genetic clades, and used the combination of cytogenetic, nuclear, and mitochondrial markers for species delimitations and taxonomic suggestions. The genus is composed of two major evolutionary groups, called here the ANSORGEI and NILOTICUS groups. The former contains four presumed species, while the latter is more diverse and we recognized nine species. Most relationships among species are not resolved, which suggests a rapid radiation (dated to early–middle Pleistocene). Further, there is an indication of reticulate evolution in Ethiopia, that is, the region of the highest Arvicanthis diversity. The distribution of genetic diversity suggests diversification in eastern Africa, followed by repeated dispersals to the west (Sudano‐Guinean savannas) and to the south (Masai steppe). We propose nomenclatural changes for Ethiopian taxa and provide suggestions for future steps toward solving remaining taxonomic questions in the genus.     

Characterization of microsatellite loci developed for <Emphasis Type="Italic">Amaranthus hypochondriacus</Emphasis> and their cross-amplifications in wild species

The present study reports isolation and characterization of 12 polymorphic microsatellite markers for Amaranthus hypochondriacus. A total of 92 alleles were detected across the 20 accessions, with an average of 7.7 alleles per locus. The observed (H _O ) and expected (H _E ) heterozygosity values ranged from 0 to 0.95 and from 0.49 to 0.92, respectively. At significance threshold (P < 0.05), nine loci deviated from Hardy-Weinberg equilibrium (HWE), whereas significant linkage disequilibria (LD) were observed between five pairs of loci. The 12 loci were successfully amplified in 18 other amaranth species representing cultivated grain and vegetable species, their putative progenitors and wild species. These results demonstrate wide potential applicability of these markers for the study of intra- and inter-specific genetic diversity as well as evolutionary relationships among cultivated and wild amaranths.     

Gen‐morph species concept—A new and integrative species concept for outbreeding organisms

The present article briefly reviewed the prevailing species concepts, especially biological, genetic, evolutionary, phylogenetic, ecological, and several taxonomic species concepts. The former five reflect the properties of species from diverse aspects and in different degrees, while taxonomic species concepts all contain more or less subjective elements, except for Hedberg's taxonomic method (not species concept). So far, there is no species concept that is both theoretically rational and practically operable. The present article outlined recent studies on the genus Paeonia L. (Paeoniaceae) in biology, particularly in morphology, biogeography, molecular phylogeny, and reproductive behavior, which provided insight into the relationship between variation of morphological characteristics and phylogeny. Taking the study on Paeonia L. as a case, referring to studies on some other plant groups, and incorporating the merits of the prevailing species concepts into our consideration, “gen‐morph species concept” is proposed here formally as new for outbreeding organisms. The new species concept has three special features: (i) a bridge linking morphological aspect with genetic and other aspects of species; (ii) proposal of a concrete morphological criterion for species definition, and (iii) considering quantitative and qualitative characteristics as equally valuable for species definition and introducing statistics into the concept to handle such characteristics. Therefore, the gen‐morph species concept is an integrative species concept, both theoretically objective and practically operable.     

A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internationally traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies, we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.