Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as “units”. Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.

A survey of lifespans in Oribatida excluding Astigmata (Acari)

This contribution provides an update on the duration of life cycles and lifespans of oribatid mites based on a literature review. The total lifespan is the sum of the immature developmental time (egg to adult) and the longevity of the adult. Most investigations were carried out in the laboratory, few were performed in the field, under field conditions and/or compared with field data. Many life cycles were investigated under different environmental influences. The life cycles of 144 oribatid species are listed. Compared with the total number of known oribatid species, this number is very low. Data for the total lifespan are given for 52 species, either from observations in the laboratory or estimated in comparison with field studies, but can only be guesses of the real lifespan. The typical lifespan of an oribatid species in temperate or boreal regions lasts between 1 and 2 years, rarely 3 years. The few investigated tropical species from laboratory experiments show generally faster development and shorter lifespans as species from temperate regions; no field studies have been carried out in the tropics yet. Long lifespan periods of 5 to 8 years are particularly characteristic of species in polar regions and in mountainous temperate regions. Some examples of species with different longevity in distinct climate regions, very long lifespans and change of life parameters under stressful laboratory conditions are presented.

The genus Oligonychus Berlese (Acari, Prostigmata, Tetranychidae): taxonomic assessment and a key to subgenera, species groups, and subgroups

A comprehensive taxonomic assessment of the most agriculturally important and highly diverse spider mite genus, Oligonychus Berlese (Acari: Tetranychidae) was performed. The sub-generic division, species groups, doubtful species, species complexes and the interpretation of a key generic character are discussed. Based on the orientation of the male aedeagus, only two subgenera, namely Oligonychus Berlese (aedeagus downturned) and Reckiella Tuttle & Baker (aedeagus upturned), are valid in the genus Oligonychus. The subgenera Homonychus Wainstein, Metatetranychoides Wainstein, and Wainsteiniella Tuttle & Baker are considered to be synonyms of the subgenus Oligonychus, whereas the subgenus Pritchardinychus Wainstein is proposed as a synonym of the subgenus Reckiella. Moreover, based on female morphological characters, four species groups (coffeae, exsiccator, iseilemae, and peruvianus) and 11 species subgroups (aceris, biharensis, coffeae, comptus, exsiccator, gossypii, iseilemae, peruvianus, pritchardi, smithi, and subnudus) are suggested in the subgenera Oligonychus and Reckiella. Fourteen Oligonychus species are proposed as species inquirendae, and potential cryptic species complexes in the genus Oligonychus are briefly highlighted. It is agreed that the clunal seta h1 is always absent, while the para-anal setae h2 and h3 are always present in the genus Oligonychus. A key to subgenera, species groups, and species subgroups of the genus Oligonychus is provided.

Exploration of the Species-specific Dna Markers Based on the Complete Chloroplast Genome for Discriminating Curcuma Comosa Roxb. From Curcuma Latifolia Roscoe and Other Related Species

Members of the Curcuma genus are among the most commonly used rhizomatous herbs worldwide. There are two species of Curcuma referred to as “Wan Chak Motluk” in Thai, C. comosa Roxb. and C. latifolia Roscoe, and their herbal materials are often confused. C. comosa is widely used as a traditional herbal remedy for its phytoestrogenic activity, but its morphology is highly similar to that of C. latifolia, which contains a compound that causes hepatotoxicity. In this study, the complete chloroplast (cp) genomes of these species were determined for the first time using Illumina sequencing. Our results showed that their cp genomes were 162,272 bp (C. comosa) and 162,289 bp (C. latifolia) in length. A total of 133 unique genes were identified, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Comparative analyses with other species of Curcuma indicated high similarity in gene content and structural organization. The analyses also reveal variable hotspots in the genomes at ndhA, trnT-trnL, and ndhC-trnV that can serve as species-specific nucleotide barcodes. Indeed, mislabeling of these two species among samples sold at market was detected using these species-specific markers, indicating that cp genomes can provide more information for better elucidating and improving discriminatory power for species authentication.

Termin "rasa" i jego synonimy w polskiej refleksji naukowej i popularnonaukowej w latach 1864–1918

The Term Race and its Synonyms in Polish Scholarly and Popular Science Thought, 1864–1918In the Polish scholarly literature concerning terminology used in different fields of knowledge, issues of the meaning and usage of the term race have not been discussed. The article aims at demonstrating how the term race was used in the Polish writings. Typically, it was in use interchangeably with terms considered as its synonyms, such as plemię, szczep, gałąź, lud and naród, as well as the notions adapted from natural sciences such as species and variety. All these terms were applied in order to categorize human groups, describe and classify them. The meaning of the notion race was not fully analyzed. Moreover, despite the fact that the Western science and its development was followed and popularized in Poland, no clear definitions appeared there. The majority of Polish authors still used the terms mentioned above as synonyms and understood quite different contents from the point of view of biology, culture and spiritual and social contexts. The term racial was still used interchangeably with such terms as ethnic, ethnographic, ethnological. Even though in the second half of the nineteenth century some Polish scholars (e.g. Ludwik Gumplowicz, Erazm Majewski, and Ludwik Krzywicki) initiated attempts to clarify this terminology, their effort did not ultimately exert an influence on the language of the message. Termin rasa i jego synonimy w polskiej refleksji naukowej i popularnonaukowej w latach 1864–1918W polskiej literaturze naukowej dotyczącej terminologii stosowanej w różnych dziedzinach wiedzy nie poruszono dotąd zagadnień związanych ze znaczeniem i użyciem terminu rasa. Celem artykułu jest ukazanie sposobu pojmowania tego terminu i zakresu jego stosowania w piśmiennictwie polskim. Najczęściej był on używany zamiennie z określeniami uważanymi za jego synonimy, takimi jak plemię, szczep, gałąź, lud i naród oraz przyswojonymi z nauk przyrodniczych: gatunek i odmiana. Wszystkie te terminy służyły rozróżnianiu grup ludzkich, ich opisowi i klasyfikacji. Nie udawało się zgłębić znaczenia pojęcia rasa. Także nauka zachodnia, którą śledzono i popularyzowano, nie przynosiła jasnych definicji. Większość z piszących stosowała synonimicznie wspomniane terminy i rozumiała pod nimi zupełnie inne treści: biologiczne, kulturowe i duchowe, społeczne. Określenia rasowy natomiast używano zamiennie z takimi wyrazami jak etniczny, etnograficzny, etnologiczny. Choć w drugiej połowie XIX wieku polscy uczeni (Ludwik Gumplowicz, Erazm Majewski, Ludwik Krzywicki) podejmowali próby uporządkowania terminologii, pozostały one bez większego wpływu na język przekazu.

Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil

Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.

panModule: detecting conserved modules in the variable regions of a pangenome graph

The recent years have seen the rise of pangenomes as comparative genomic tools to better understand the evolution of gene content among microbial genomes in close phylogenetic groups such as species. While the core or persistent genome is often well-known as it includes essential or ubiquitous genes, the variable genome is usually less characterized and includes many genes with unknown functions even among the most studied organisms. It gathers important genes for strain adaptation that are acquired by horizontal gene transfer. Here, we introduce panModule, an original method to identify conserved modules in pangenome graphs built from thousands of microbial genomes. These modules correspond to synteny blocks composed of consecutive genes that are conserved in a subset of the compared strains. Identifying conserved modules can provide insights on genes involved in the same functional processes, and as such is a very helpful tool to facilitate the understanding of genomic regions with complex evolutionary histories. The panModule method was benchmarked on a curated dataset of conserved modules in Escherichia coli genomes. Its use was illustrated through a study of a high pathogenicity island in Klebsiella pneumoniae that allowed a better understanding of this region. panModule is freely available and accessible through the PPanGGOLiN software suite (https://github.com/labgem/PPanGGOLiN).

Determination of arsenic, cadmium, selenium, zinc and other trace elements in Bangladeshi fish and arsenic speciation study of Hilsa fish flesh and eggs: Implications for dietary intake

Exposure to As from drinking water and its impact on the health of the Bangladeshi population has received much attention. However, very little information is available regarding As exposure through consumption of fish, which is the main source of animal protein for the majority of Bangladeshis. In this study, concentrations of As, Cd, Pb, Mn Se and Zn in different types of fish, consumed by Bangladeshis, were determined using Inductively Coupled Plasma Mass Spectrometry. Daily intakes of the toxic elements As, Cd and Pb through fish consumption were estimated to be 31.8, 0.4 and 4.8 μg/day, respectively. Hilsa (Tenualosa ilisha) contained the highest concentrations of total As (mean ± SD was 2.55 ± 1.3 mg/kg; n = 15) among the fish analysed. However, toxic inorganic As species were not detected. The dominant As species in Hilsa fish were: dimethylarsenic acid, arsenobetaine and arsenosugars, at 69, 11 and 20% of total As, respectively. The high concentration of Cd detected in Hilsa eggs (average 278 ± 518 μg/kg; range 7.4–1725 μg/kg; n = 10) is of concern since this may have harmful effects on the development of embryos and lead to a decline in the Hilsa population or the quality of the fish. It can also be harmful to those who consume Hilsa eggs on a regular basis. Selenium was found to be highest in Shoal (Micropterus cataractae) fish and a type of small fish, and lowest in Mrigal (Cirrhinus cirrhosis). Small fish species contained Mn and Zn at 7.1- and 4.3-fold higher concentrations, respectively, compared to big fish species. Keski (Corica soborna), a small fish species, contained by far the highest concentrations of Mn (52 mg/kg) and Zn (140 mg/kg), although the concentration of As (1.4 mg/kg) in this fish was lower than that of several other fish species. Small fish species are often consumed whole, including the bones, and therefore the essential trace elements present are potentially bioavailable for cellular metabolism. Our study shows that the Bangladeshi population can easily meet their daily requirement of Se and Zn from consumption of fish such as Shoal fish (Se and Zn), Hilsa fish (Se and Zn) and Keski fish (Se and Zn). Consumption of small fish (such as Keski) and big fish (such as Hilsa) from Bangladesh can provide valuable sources of essential trace elements as part of a balanced diet and thus negate the need for supplements and biofortification of certain foods. Ours is a small study and a detailed total dietary intake and human biomonitoring studies, that includes coverage of different socio-economic groups, are needed in Bangladesh before giving people supplements or biofortified foods.

The Story of the Tulip That Went Wild: Tracing the History of Introduction of Tulipa Sylvestris in Sixteenth-Century Europe

Tulipa sylvestris, commonly called the “wild tulip”, was introduced from the Mediterranean to northern Europe in the sixteenth century and became widely naturalized. Research has focused on tulips that came from the Orient, but the introduction path of this native European, early ornamental tulip is unclear, and so is its taxonomic status: three subspecies are provisionally accepted, sometimes treated as species. Here we elucidate the history of introduction of T. sylvestris and discuss its taxonomy based on our historical findings. The first bulbs came from Bologna (northern Italy) and Montpellier (southern France) in the 1550s-1570s. Several renown botanists were involved in their introduction, namely Gessner, Wieland, Aldrovandi, De Lobel, Clusius, and Dodoens. There were various introduction routes, including one from Spain which was apparently unsuccessful. The strong sixteenth-century Flemish botanical network facilitated the introduction and naturalization of T. sylvestris across Europe. Based on the latest tulip taxonomy, the diploid subspecies australis is native in the Mediterranean, and the tetraploid sylvestris is naturalized over Europe, but our historical findings show that both sylvestris and australis were introduced. This underlines the need to reconsider the taxonomic status of T. sylvestris, highlighting the importance of botanical history in understanding the complex taxonomy of naturalized cultivated plants.

Evolutionary and allometric insights into anuran auditory sensitivity and morphology

As species change through evolutionary time, the neurological and morphological structures that underly behavioral systems typically remain coordinated. This is especially important for communication systems, in which these structures must remain coordinated both within and between senders and receivers for successful information transfer. The acoustic communication of anurans (“frogs”) offers an excellent system to ask when and how such coordination is maintained, and to allow researchers to dissociate allometric effects from independent correlated evolution. Anurans constitute one of the most speciose groups of vocalizing vertebrates and females typically rely on vocalizations to localize males for reproduction. Here, we compile and compare data on various aspects of auditory morphology, hearing sensitivity and call dominant frequency across 81 species of anurans. We find robust, phylogenetically independent scaling effects of body size for all features measured. Furthermore, after accounting for body size, we find preliminary evidence that morphological evolution beyond allometry can correlate with hearing sensitivity and dominant frequency. These data provide foundational results regarding constraints imposed by body size on communication systems and motivate further data collection and analysis using comparative approaches across the numerous anuran species.