Molecular Phylogenetic Studies Research Articles

Identifying potential adaptive SNPs within combined DNA sequences in Genus Crocus L. (Iridaceae family): A multiple analytical approach

The genus Crocus L. of Iridaceae family contains about 160 species and is considered as a complex group of plant taxa with regard to evolutionary and phylogenetic events. Inter-specific hybridization and gene flow contribute to species genetic homogeneity in one hand and high within species genetic variability and species genetic content overlaps caused species resolution a problem. In spite of extensive molecular phylogenetic studies in this genus, nothing is known about DNA sequences or Single nucleotide polymorphisms (SNPs) which are of adaptive nature. Moreover, nothing is known about which geographical or environmental factors plays role in species local adaptation and speciation events within Crocus L. genus. Therefore, the present study was conducted to answer the above said questions. We used a combined molecular data set of internal transcribed spacer (ITS) nuclear gene and trnL-F intergenic spacer (trnL-F) sequences of chloroplast genome. A multiple analytical method of Canonical correlation (CCA), Redundency analysis (RDA), and Latent Factor Mixed Model (LFMM)identified a few potential adaptive SNPs. Moreover, population criterions like Tajimas’ D, molecular clock test, as well as skyline-plot revealed a smooth and continuous genetic changes for most of the Crocus species, but the occurrence of a sudden deep nucleotide substitution for Crocus taxa of Iran. The impact of latitude was significantly higher on nucleotide changes compared to that of longitudinal distribution of Crocus species.

Molecular phylogenetics of Maranta (Marantaceae: Zingiberales): non-monophyly and support for a wider circumscription

Abstract Neotropical Maranta has repeatedly emerged as non-monophyletic in molecular phylogenetic studies, but no taxonomic changes have been proposed due to previous weak support for the main clades and overall sparse taxonomic sampling. Our study includes a phylogenetic hypothesis strictly based on molecular evidence, using nuclear ribosomal (nrITS) and plastid (rps16, trnL-F and rpl32-trnL) markers for Maranta and allied genera. Thirty-two species from eight genera were sampled, and maximum likelihood (ML) and Bayesian inference (BI) analyses were carried out. Non-ambiguous indels were scored in both analyses to test their contribution to internal support. Our results confirm that Maranta, as previously delimited, is non-monophyletic, with species of Hylaeanthe, Myrosma and Koernickanthe nested among clades of Maranta. The combined BI analysis without indels was the best resolved, and inclusion of indels increased support only for terminal clades. The sampled species comprise two sister clades, one with Maranta + Hylaeanthe + Myrosma + Koernickanthe and the other with Ctenanthe + Saranthe + Stromanthe. The infrageneric classification proposed by Schumann for Maranta (M. subgenera Maranta and Calateastrum) is partially corroborated by our results, but the remaining subgenera need to be further studied. Based on our strongly supported phylogenetic results, we revise the taxonomy of these genera, expanding the limits of Maranta. We propose two new combinations and a new name for Hylaeanthe in Maranta.

Morphological and Molecular Characterization of Talanema eshtiaghii sp. n. (Dorylaimida, Qudsianematidae) from Iran.

A new species of the genus Talanema, recovered from the northwest of Iran, was described based on morphological, morphometric, and molecular data. Talanema eshtiaghii sp. n. was characterized by its 1.45-1.68 mm long body, lip region offset by constriction and 13-15 μm wide, odontostyle 15-18 μm long, double guiding ring, neck 312-362 μm long, pharyngeal expansion occupying 41-43% of the total neck length, uterus tripartite, and 111-189 μm long or 2.1-3.2 body diameters, vulva transverse (V = 55-58), tail similar in both sexes, conical with a dorsal concavity (30-44 μm, c = 33-56, c' = 1.0-1.6), spicules 49-56 μm long, and 14-18 shortly spaced ventromedian supplements in front of the level of the anterior end of spicules, with distinct hiatus. It was compared to four closely similar species, with emphasis on the most relevant traits to distinguish them. Molecular phylogenetic studies using partial sequence of the 28S rDNA (D2-D3 segment) revealed that the new species forms a clade with other currently sequenced representatives of Talanema, tentatively supporting the monophyly of this genus.

Cryptic diversity in Zoraptera: Latinozoros barberi (Gurney, 1938) is a complex of at least three species (Zoraptera: Spiralizoridae).

The order Zoraptera contains relatively few species, but current molecular phylogenetic studies suggest an unexpectedly high level of cryptic diversity in the order with many overlooked species based on morphology alone. Latinozoros Kukalova-Peck & Peck, 1993 represents the only genus of monotypic Latinozorinae (Zoraptera: Spiralizoridae) with only one species described, L. barberi (Gurney, 1938), until now. Although this species has been repeatedly reported from a number of locations in South and Central America, it is likely a complex of unrecognized species. Here, we present a molecular phylogenetic reconstruction revealing three genetically distinct lineages in Latinozoros, and we also present detailed morphological comparisons that prove the species status of Latinozoros cacaoensis sp. nov. from French Guiana and L. gimmeli sp. nov. from the Dominican Republic, Trinidad and Panama. The results indicate that the species previously referred to L. barberi is actually a species complex that includes L. barberi, the new species described here, and perhaps other species.

Wood and bark structure in Buddleja: anatomical background of stem morphology.

Bark (all tissues outside of the vascular cambium) has been extensively studied in recent years, especially its anatomy and physiology. Macromorphological bark characters can be important taxonomically for many plant groups, including the genus Buddleja (Scrophulariaceae). However, the relationship between macroscopic bark appearance and its microscopic structure remains obscure, hampering the use and interpretation of bark traits in plant taxonomy and phylogenetics as well as in other fields of botany. We studied micro- and macrostructure of bark in the species of Buddleja representing wide taxonomic and geographic diversity to identify general relationships between bark anatomy and morphology. We also examined Buddleja xylem and discussed the importance of anatomical traits for understanding the relationships between clades in this genus. The smooth bark surface in sect. Gomphostigma and the outgroup (Freylinia spp.) relates to the small number of periderms of superficial origin and limited sclerification. This allows for the retention of visible lenticels. In the rest of Buddleja, bark sloughs off and division of labour is present: collapsed phloem undergoes sclerification and acts as a protective layer, while thin-walled phellem forms the separation layers. A similar pattern is found in some groups (e.g. Lonicera), but in others (e.g. Vitis and the species of Eucalyptus with stringy bark), the pattern is inversed. Wood and bark anatomy supports a sister relationship between the southern African section Gomphostigma and the rest of Buddleja but is taxonomically uninformative among remaining clades. Limited development of periderms and sclerification allows for the retention of a smooth bark surface and conspicuous lenticels. Sloughing off of bark requires division of labour into a lignified protective layer and a thin-walled separation layer. These two functions are never served by a single tissue but are rather divided between phloem and periderm. How more subtle features (e.g. size and shape of fissures) are determined requires further study. Simultaneously, bark anatomy could be a useful source of data to complement molecular phylogenetic studies in a total evidence approach for systematics.

A new perspective on the macrolichen genus Platismatia (Parmeliaceae, Ascomycota) based on molecular and phenotypic data

Lichens in the genus Platismatia are common, widespread and were some of the first to be studied by Western taxonomists. However, few molecular phylogenetic studies of Platismatia have been published to date. We present an expanded phylogeny of Platismatia inferred from 60 newly generated ITS sequences and 28 existing publicly available sequences. The new phylogeny confirms the delimitation of P. wheeleri as monophyletic and distinct from the widespread P. glauca, the latter of which was recovered as two separate, highly supported clades, that do not appear to differ in phenotype or biogeography. The western North American endemics P. herrei and P. stenophylla were not recovered as reciprocally monophyletic and may be an example of recent speciation similar to that also hypothesized for Alectoria in the same region. Ancestral state reconstructions of reproductive modes (dominant asexual vs. sexual reproduction; asexual propagule type) suggest that sexual species like P. tuckermanii can evolve from primarily asexual ancestors. Evaluation of species distributions suggests that reproductive mode may be related to range size. These data suggest that Platismatia could serve as a model for future studies on reproductive mode, biogeography and speciation in lichens.

Taxonomic revision and re-description of Ateuchosaurus pellopleurus (Hallowell, 1861) (Reptilia, Squamata, Scincidae) with resurrection of A. okinavensis (Thompson, 1912)

The scincid lizard Ateuchosaurus pellopleurus (Hallowell, 1861) has been recognized as a single species widely distributed in the Osumi, Tokara, Amami, and Okinawa Groups of the Ryukyu Archipelago, southern Japan. However, a recent molecular phylogenetic study suggested that this skink should be divided into two species: one distributed in the Osumi to Amami Groups, and another distributed in the Okinawa Group. For A. pellopleurus, two extant syntypes collected from an island of the Amami Group were confirmed. Therefore, we identified the species in the Osumi to Amami Groups as A. pellopleurus sensu stricto by designating one of the syntypes as the lectotype for this species. For the species in the Okinawa Group, we resurrected A. okinavensis (Thompson, 1912), of which the type locality is on Okinawajima Island in the Okinawa Group. Ateuchosaurus pellopleurus and A. okinavensis can be differentiated by the following characteristics: usually separated frontonasal and frontal, 8–14 subdigital scales on the fourth toe (mode = 11), and usually two or three pairs of dorsal median scale rows with black stripes in A. pellopleurus; usually fused frontonasal and frontal, 10–16 subdigital scales on the fourth toe (mode = 13), and usually no stripe on the dorsal scales or a pair of dorsal median scale rows with black stripes in A. okinavensis.

Phylogenetic Relationships in the Group Caespitosa of Paspalum L. (Poaceae, Panicoideae, Paspaleae)

The informal group Caespitosa of Paspalum L. comprises 13–15 perennial species that are able to tolerate extreme climatic stresses, such as prolonged droughts, floods, and saltwater. Previous molecular phylogenetic studies have suggested that the Caespitosa might not be monophyletic, but they did not analyze a large enough sample of taxa for a meaningful conclusion. In this study, we evaluate the phylogeny of the genus Paspalum using parsimony, likelihood, and Bayesian inference based on four DNA regions (ETS, ndhF, rpl16, and trnH-psbA) and increasing the number of sampled species (i.e., a total of 13 taxa and 40 new accessions of the group Caespitosa). Our main objective was to analyze the positions of Caespitosa taxa, assuming a priori that they do not represent a natural group as traditionally circumscribed. Our findings showed the Caespitosa species distributed in seven morphologically distinct clades and correlated with members of the informal groups Alma, Corcovadensia, Dissecta, Lachnea, Macrophylla, Notata, Paniculata, and Rupestria. Clades containing Caespitosa taxa were characterized based on morphological, anatomical, and cytological evidence, one of which was associated with geographic isolation. A comparison with results from other studies, a brief discussion on the group Macrophylla, which our analyses showed to be polyphyletic, and comments on the need for future molecular studies in Paspalum are also included.

New subgeneric names for the most commercially important shrimp genus Penaeus Fabricius, 1798 (Crustacea, Decapoda, Penaeidae).

Although a recent comprehensive molecular phylogenetic study on Penaeus Fabricius, 1798 reinstated a single genus for these economically important shrimps, several clades in the molecular phylogenetic tree do not have formal names. Subgeneric names are given herein to five of these clades if Penaeus is to be split. A key to the subgenera in Penaeus is also provided.

New data on the Austropotamobius torrentium (Schrank, 1803) from the tributaries of the Bosna River

The crayfish Austropotamobius torrentium is a dominant species of the family Astacidae in the rivers of the Black Sea and Adriatic basins of Bosnia and Herzegovina. Molecular phylogenetic studies in Europe revealed the presence of eight phylogroups. No morphometric and meristic characteristics have been determined that would clearly separate them. The paper presents new data on the morphometric parameters species Austropotamobius torrentium with watercourses Presjenica, Jošanica and Crna Rijeka. This analysis is based on 22 parameters that were measured on 38 crayfish individuals, whose size was larger than 5 cm. Using Anova test, Bonfferoni test and discrimination analysis, it was determined that females differ significantly in a small number of parameters, while males showed greater morphological divergence. The great diversity of habitats of Austropotamobius torrentium in Bosnia and Herzegovina obliges the inclusion of the Dinarides region in molecular phylogenetic studies. This will result in more precise and complete data on Austropotamobius torrentium populations.

Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence.

Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000-4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.

New data on pollen morphology of the genus Camphorosma (Chenopodiaceae)

Recent molecular phylogenetic studies of Camphorosmoideae (Chenopodiaceae) demonstrated that Camphorosma is monophyletic. Palynomorphological peculiarities are used in taxonomy as additional diagnostic features and pollen analysis. Pollen morphology was studied using light and scanning electron microscopy, based on 13 specimens belonging to four species (C. annua, C. lessingii, C. monspeliaca and C. songorica). The aim of this research was to provide new data on pollen characteristics of the above mentioned species and to evaluate their taxonomic value. The results obtained show that pollen grains are pantoporate, spheroidal, circular in outline, undulate or slightly undulate on the edges; small or medium-sized. Pores are circular, with distinct margins. Exine sculpture is nanoechinate, tectum psilate or psilate-perforate. Pore membranes are nanoechinate. Taxonomic relevance of the most important characters of pollen grains (pollen diameter, pore number, pore diameter, distance between pores and between pore centres, C/D value, nanoechini density, presence/absence of perforations, number of nanoechini on pore membranes, structure of columellae) is discussed. The exine structure of pollen grains of all species was analysed for the first time in the current study. Pollen morphology proved to be an important additional source of information for taxonomy for species-specific identification and pollen analysis within Camphorosma. Palynomorphological data are interpreted in the existing phylogenetic framework.

A checklist of Erebinae (Lepidoptera, Erebidae) from India

Species under the subfamily Erebinae in India has been compiled and updated. A total of 250 species under 65 genera is enumerated. Current systematic status of the species based on the molecular phylogenetic studies by Zahiri et al. (2011) is given along with their type species and generic synonyms.

Pollen morphology of selected taxa of Valeriana (Caprifoliaceae): taxonomic and evolutionary implications

Pollen morphology of 34 herbarium specimens belonging to 17 taxa of the genus Valeriana was studied using light and scanning electron microscopy. The aim of this research was to evaluate the taxonomical value of palynomorphological data for species-specific identification. Pollen grains are monads, radially symmetrical, isopolar, tricolpate, oblate to prolate (P/E = 0.69–1.59); medium- or large-sized (P = 26.60–66.50 µm; E = 23.94–57.19 µm). Colpi are long, medium-length or short, with acute, obtuse or rounded ends. Four types and eight subtypes of exine sculpture were recognised: type I—echinate-verrucate (5 spp.), type II—echinate-nanoechinate-verrucate (10), type III—echinate-microechinate-nanoechinate-verrucate (1), type IV—echinate-microechinate-nanoechinate (1). Additional characters of taxa of Valeriana diagnostic at species level for the purposes of taxonomy are: size of pollen and colpi, exine sculpture: presence/absence of verrucae, their form, size and form of echini/microechini/nanoechini, their number, pattern of tectum in areas between echini, exine thickness in mesocolpia and apocolpia. Our palynomorphological data support the results of molecular phylogenetic studies. The close phylogenetic relationships of the species V. montana, V. tripteris, V. supina and V. pyrenaica are also supported by their palynomorphological characters, such as exine sculpture (type I). Cluster analysis mainly supports the definition of pollen types and subtypes (based on qualitative data), since species are grouped as five separate branches. The pollen grains of five taxa were analysed for the first time in the current study.

Complete chloroplast genome and phylogenetic analysis of Anemone shikokiana.

Anemone shikokiana (Makino) Makino, disjunctly distributed in Shandong Peninsula of China and Shikoku Island of Japan, is a rare and endangered species. To provide genetic information and understand its phylogeny, we conducted research on the chloroplast (cp) genome of A. shikokiana. The complete cp genome sequence of A. shikokiana was constructed in this study. The results showed that the cp genome of A. shikokiana has a typical quadripartite cyclic with a total length of 159,286bp. In total, 111 unique genes were identified, including 78 protein-coding genes, 29 tRNA-coding genes and 4 rRNA-coding genes. A total of 37 long repeat sequences and 67 microsatellites were found in this cp genome. The cp genome of A. shikokiana was compared with eleven other Anemone cp genomes available from the Genbank database. We found some variations among the different genomes, especially in the LSC and SSC regions, and identified some regions as potential molecular markers such as ycf1, ndhE, ndhD, ndhF-trnL, ndhA and ndhF. The results of phylogenetic analysis suggested that A. narcissiflora was the closest relative of A. shikokiana. The results filled the gap of cp genome sequence information of A. shikokiana, laying the foundation to explore the evolutionary relationships of A. shikokiana in future studies. It provided a valuable genetic resource for the molecular identification and phylogenetic study of Anemone.

Recircumscription of Utricularia leptorhyncha and U. lasiocaulis and three related new species for northern Australia

The Utricularia lasiocaulis F.Muell. complex (subg. Polypompholyx; sect. Lasiocaules) is a morphologically and ecologically variable group of closely related taxa with a mostly tropical distribution across northern Australia. A recent molecular phylogenetic study placed the recognised species U. kamienskii F.Muell. sister to a clade of accessions relegated to either U. leptorhyncha O. Schwarz or U. lasiocaulis, with the latter previously circumscribed as an assemblage of highly variable morphological forms. We have expanded the previous study to include populations representing the known distributions of all three species and have attempted to include all morphological variants; 55 ingroup accessions were used in the full phylogenetic analysis based on two non-coding chloroplast regions (rps16, trnD–T) and the nuclear ribosomal internal transcribed spacer (ITS). We found that the pink corolla form of the usually white flowered U. kamienskii is not sufficiently different, and we retain it under that species. We also found strong support for a paraphyletic U. leptorhyncha, with the smaller flowered accessions matching the type material placed sister to all other U. lasiocaulis forms, including a grouping previously assigned as a larger flowered U. leptorhyncha. Within the U. lasiocaulis clade we found that much of the variation sorts into well-supported clades that we find are sufficiently morphologically and genetically differentiated from the type clade for recognition at the specific rank, namely Utricularia brennanii R.W.Jobson & Baleeiro from Northern Territory and Queensland, Utricularia cowiei R.W.Jobson & Baleeiro from the Kimberley region of Western Australia, and U. disjuncta R.W.Jobson & Baleeiro restricted to the Darwin and Gulf region of the Northern Territory.

Illusion of flight? Absence, evidence and the age of winged insects

Abstract The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.

Phylogenetic Placement and Taxonomic Revision of the Genus Monochilus (Lamiaceae), a Rare Brazilian Endemic

Abstract— Monochilus (Lamiaceae) is an enigmatic genus endemic to Brazil with two rarely collected species currently recognized. Based on morphological features Monochilus is hypothesized to be closely related to Amasonia within subfamily Ajugoideae. However, Monochilus is one of the few genera within Lamiaceae never to be represented in a published molecular phylogenetic study, and thus has an uncertain placement with the subfamily. During recent herbarium exploration in association with the Flora of Brasil 2020 project, new specimens of Monochilus gloxinifolius and M. obovatus were uncovered. Based on this material, a new phylogeny of Ajugoideae was constructed based on nuclear ribosomal ITS and chloroplast matK and trnL-trnF markers. Monochilus, as previously hypothesized, is closely related to Amasonia and placed within Ajugoideae. We discuss the phylogenetic placement of the genus and provide a taxonomic revision with description, distribution maps, an identification key, preliminary conservation assessments, photographic plates, and comments on both the taxonomy and ecology of these two species. Additionally, we provide a lectotypification for M. gloxinifolius.

Deep-sea hydrozoans in the western part of the Bering Sea: some hydroids associated with methane seep communities at upper bathyal depths and abyssal hydroids with a description of two new species

Seven hydrozoan species were collected from the abyssal depths of the Volcanologists Massif and Komandorsky Basin (∼3360–3930 m) and from methane seep communities on the Koryak slope at upper bathyal depths (∼660 m) during the cruise of the RV Akademik M.A. Lavrentyev in 2018 in the western part of the Bering Sea. Hydroids were used for detailed morphological analysis and identified using mitochondrial (16S rRNA) and nuclear (18S, 28S) markers. Two new species of large hydroids, Branchiocerianthus radialis sp. nov. and Candelabrum beringensis sp. nov., were described from the abyssal depths. Branchiocerianthus radialis sp. nov. has an unusual radial symmetry, uncharacteristic for this genus. However, molecular phylogenetic data and dichotomous branched blastostyles unequivocally indicate its belonging to the genus Branchiocerianthus. Candelabrum beringensis sp. nov. differs from C. phrygium, widespread in the Northern Hemisphere, by the root-like foot zone covered by multiple tentacle-like suckers and rare specialized tentacles. Earleria cf. denticulata is most likely a wide spread species inhabiting bathyal and abyssal biotopes in the Pacific and Atlantic Oceans. Cryptic biodiversity was found for phylogenetic clade Lafoea cf. dumosa sp. 2, including two species from bathyal and abyssal depth of the Bering Sea. Methane seep communities were locations with enhanced diversity of hydroids and were inhabited by numerous so called “hydroid bushes” dominated by species L. cf. dumosa (presumably L. cf. dumosa/sp. 2C, Lafoeidae) and various sertulariids attached to carbonate crusts and pebbles. Four species from the methane seep communities were analyzed in detail and identified basing on molecular data: L. cf. dumosa/sp. 2C, Abietinaria cf. kinkaidi, Tubularia sp. and Hydrodendron cf. stechowi. Phylogenetic position of two species was unexpected: A. cf. kincaidi (Sertulariidae) showed no relationship with available Abietinaria spp. and grouped with sertulariid Thuiaria thuja, and H. cf. stechowi currently assigned to Phylactothecidae grouped with the species of the family Zygophylacidae. Our results confirm the presence of hard-to-identify hydrozoan species (Lafoea spp., Earleria spp., Candelabrum spp.) that differ at different depths. Therefore careful morphological and molecular phylogenetic studies are needed for species identification of deep-sea specimens.

A new subfamily taxon for Sasia and Verreauxia (Picidae)

A review of eight molecular phylogenetic studies supports the distinctiveness of the genera Sasia/Verreauxia from Picumnus and casts doubt on the monophyly of Picumninae. We propose to restrict Picumninae to Picumnus and to place Sasia and Verreauxia in a new subfamily, Sasiinae.