Carya illinoinensis (Juglandaceae): A new genus and species for the flora of Pakistan

Reappraising adaptive radiation

Irrigation with RO concentrate and brackish groundwater impacts pecan tree growth and physiology

Davalliaceae have been classified on the basis of morphological data or morphological and molecular data. The family has been divided into various genera, the circumscription of which may differ between authors. Previous phylogenetic analyses used limited numbers of genes and taxa. We studied the molecular phylogeny of the family by using two nuclear markers (LEAFY intron 1, gapCp intron) and a long chloroplast marker (atpB‐rbcL‐accD) in 55 specimens of 41 species. The results indicated that Davalliaceae are divided into seven clades, six of which coincide with the genera and sections sensu Kato & Tsutsumi. The relationships among the clades were inconsistent with respect to the markers analyzed, and a species tree derived from all datasets did not resolve the relationships. In addition, the clades were not well characterized to be classified at the genus level. Therefore, we propose to classify Davalliaceae in the single genus Davallia with seven sections, i.e., sect. Araiostegiella, sect. Davallia (comprising only D. canariensis), sect. Davallodes (including Araiostegia p.p. and Paradavallodes), sect. Humata (including Pachypleuria and Parasorus), sect. Scyphularia (s.l. = sect. Davallia sensu Kato & Tsutsumi excluding the type), sect. Trogostolon (s.l. = sect. Trogostolon sensu Kato & Tsutsumi), and sect. Cordisquama (s.l. = Wibelia sensu Kato & Tsutsumi). A key to the sections and a table of characters for the sections are provided.

The United States is a major supplier in the world pecan market. Using grower-level pecan price data from the 2005–2016 seasons, we estimate pecan market integration patterns among Texas, Oklahoma, Georgia, and Louisiana using causality structures identified through cutting-edge machine-learning methods. Current pecan price received by growers in Texas is a direct cause of those in Oklahoma, Georgia, and Louisiana. Past-period grower-level pecan price in Georgia either directly or indirectly influences the current price in other states. These findings are useful for businesses and the government in order to price and promote marketing of pecan.

In the fall 2021, red table beet plants (Beta vulgaris L. cv 'Eagle') exhibiting stunted growth with shorter petioles were observed at an incidence of 10 to 15 percent in a production field in Payette County, Idaho, United States. In addition to stunting, beet leaves displayed yellowing and mild curling and crumpling, and the roots exhibited hairy root symptoms (sFig.1). To identify potential causal viruses, total RNA was isolated from the leaf and root tissue using RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and subjected to high-throughput sequencing (HTS). Two libraries were prepared, one for the leaf sample and another for the root sample using a ribo-minus TruSeq Stranded Total RNA Library Prep kit (Illumina, San Diego, CA). HTS was performed with 150 bp paired-end sequencing on a NovaSeq 6000 (Novogene, Sacramento, CA). Following adapter trimming and removal of host transcripts, 5.9 and 16.2 million reads were obtained from the leaf and root samples, respectively. These reads were de novo assembled using the SPAdes assembler (Bankevitch et al., 2012; Prjibelski et al., 2020). The assembled leaf sample contigs were aligned to the NCBI non-redundant database to identify contigs matching known viruses. A single contig of 2845 nts that shared 96% coverage and 95.6% sequence identity to the pepper yellow dwarf strain of beet curly top virus (BCTV-PeYD, EU921828; Varsani et al., 2014), and 98% coverage and 98.39% identity with an isolate of BCTV-PeYD (KX529650) from Mexico, was identified in the leaf sample (GenBank Accession OP477336). To validate the HTS detection of BCTV-PeYD, total DNA was isolated from the leaf sample and a 454 bp fragment of the C1 gene (replication-associate protein) was PCR amplified and Sanger sequencing of the amplicon revealed 99.7% identity to the HTS assembled BCTV-PeYD sequence. In addition to the PeYD strain of BCTV, the Worland strain of BCTV (BCTV-Wor) was detected as a single 2930 nt contig with 100% coverage and 97.3% identity to the BCTV-Wor isolate CTS14-015 (KX867045) known to infect sugar beet in Idaho. Of note, there are 11 strains of BCTV and among those, the BCTV-Wor strain induces mild symptoms in sugar beet (Strausbaugh et al., 2017), whereas BCTV-PeYD was found only in pepper from New Mexico. Further, two contigs of 2201 nts and 523 nts were assembled generating a nearly complete genome of spinach curly top Arizona virus (SpCTAV) in the leaf sample with 99% coverage and 99.3% identity (GenBank Accession OQ703946) to the reference genome of SpCTAV (HQ443515; Hernandez-Zepeda et al., 2013). To validate the HTS results, total DNA was isolated from the leaf tissue and PCR amplified a 442 bp fragment that overlaps the V1, V2, and V3 ORFs and its sequence revealed 100% identity with the HTS assembled SpCTAV. The roots sample also showed HTS reads corresponding to BCTV-PeYD and SpCTAV. In addition, beet necrotic yellow vein virus (BNYVV) was detected in the root sample with 30% coverage, but no sequence reads matching to BNYVV was detected in the leaf sample. BNYVV is known to infect sugar beet causing rhizomania (Tamada et al., 1973; Schirmer et al., 2005). To further confirm the BNYVV HTS results, total RNA was extracted separately from the root and leaf tissue, and RT-PCR was performed with primers that were designed to amplify portions of BNYVV RNAs (Weiland et al., 2020). RT-PCR analysis generated the appropriate amplicons with expected sequences corresponding to the RNA-1, RNA-2, RNA-3, and RNA-4 of BNYVV as determined by Sanger sequencing implying BNYVV the causal agent of hairy root symptoms. Similar to observations seen for BNYVV infection in conventional sugar beet varieties, no amplification was detected for BNYVV in the RNA extracted from leaf tissue, indicating that the RT-PCR results are consistent with the HTS analysis. This is the first report of BCTV-PeYD and SpCTAV observed naturally infecting red table beet in Idaho suggesting the geographical expansion of these viruses. The co-existence of BCTV-PeYD and SpCTAV with limited host range needs to be investigated to determine the actual cause of the observed foliar symptoms. This report provides the basis for further research to understand the pathogenic nature of these viruses and their potential threat to red table beet and sugar beet production in Idaho.

A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus clade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s., and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia clade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Réunion, Mauritius), and the Seychelles (Mahé). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker (trnL-F) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea, which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Réunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level (Costularia baronii and Costularia robusta). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species.

The major temperate nut crops grown in different parts of the world include almond, walnut, pecan nut, chestnut, hazelnut and pistachio nut. The geographical features and agro-climatic conditions prevailing in the entire United States of America, China, Turkey and Iran are conducive for the cultivation of temperate nut crops. A continuous increase was observed in the area, production and export of all the temperate nuts crops in the last 5–6 years. In 2020, the United States of America is the leading producer of almond and pistachio nuts, while China is the leading producing country of walnut and chestnut. Mexico and Turkey were the leading producers of pecan nut and hazelnut, respectively. The United States of America (almond, walnut, pistachio nut, pecan nut), Spain (almond), Mexico (pecan nut), Turkey (hazelnut), China (walnut, chestnut, pistachio nut), Italy (hazelnut, chestnut) and Iran (pistachio nut) are the exporting countries of temperate nut crops. All the European countries are importers of all major temperate nut crops.

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record.

As a consequence of there being several ways in which observed patterns of variation in nature can be conveyed in a generic classification, long recognised genera have changed in size over time. The generic rank has its origins in folk taxonomy, where genera were homogenous units of relatively few kinds. In the era of Bentham there was a widespread preference for large genera, many of which were split during the 20th century. In a survey of contemporary (1998–2007) generic delimitation practice we found a significant dichotomy between studies that incorporate molecular data and those that rely exclusively on morphological data. The former lead to delimitation of larger genera whereas the latter in general do not. This finding spurred a broader investigation into what drives changes in overall generic sizes, new data sources or new concepts? Two new data types have been introduced during the course of history: detailed morphology (anatomy, cytology) and chemical data (amino acid and DNA sequence data). Conceptual development has seen several turns: from language and communication, through memory and stability, to evolution and monophyly. We argue that conceptual change has a greater impact than changes in data do, since new data must be interpreted and translated into a classification and since conceptual changes may spur a search for new kinds of data. We conclude that the current trend toward recognising larger genera is a result of a return to study on a broad scale, rather than of incorporation of molecular data.

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

The objectives of this study were to evaluate the leaching, degradation, uptake, and mass balance of indaziflam, as well as its potential to produce phytotoxicity effects on young pecan trees. Pecan trees were planted in pots with homogeneous porous media (sandy loam soil), preferential flow channels open to the soil surface, and shallow tillage at the soil surface. Pots were treated with indaziflam at two application rates of 25 and 50 g a.i./ha in 2014 and 2015. Each pecan tree was irrigated with 7 L of water every 2 weeks during the growing season. An irrigation volume of 2 L was used to maximize indaziflam retention time in the soil from Dec. 2015 until the end of the trees’ dormant stage. In 2014, leachate samples were collected after each irrigation for quantifying indaziflam mobility. Soil samples were collected at depths of 0 to 12 and 12 to 24 cm after 45, 90, and 135 days of indaziflam application, and leaf samples were collected at the end of the growing season to quantify mobility and uptake. Indaziflam was detected in leachate samples, and the leaf indaziflam content increased with increasing application rate. Indaziflam and its breakdown products were detected at both sampling depths. Mass recovery and half-life values for indaziflam in the soil ranged from 38% to 68% and 63 to 99 days, respectively. No phytotoxicity effects were observed from increasing application rate and retention time of indaziflam in the soil. Most of the applied indaziflam was retained in the soil at shallow depth.

Ulva (Ulvophyceae, Chlorophyta) is common in intertidal environments and can also be found in freshwater ecosystems. The difficulty to morphologically identify Ulva species due to cryptic diversity and morphological plasticity has caused a taxonomic conundrum. Fortunately, molecular data have begun to unravel a better understanding of its diversity. Here, we present a molecular analysis with 247 samples of Ulva from the Gulf of Mexico and Atlantic USA based on chloroplast (rbcL and tufA) and nuclear (ITS1-5.8S-ITS2) molecular markers. Twenty-four Ulva taxa had previously been reported for this area based on morphology and earlier molecular studies mostly from Northeastern USA and Canada. In this study, sixteen Ulva clades were identified representing 13 named clades and putatively three undescribed species. Only nine of the 24 taxa previously reported for the Western Atlantic were confirmed. Four species were identified for the first time in the U.S. East and Gulf Coast (U.aragoënsis, U.californica, U.meridionalis, and U.tepida). This study provides a foundation for future research on Ulva in this area and reiterates the necessity of using molecular-assisted identifications for this group.

Morphological and molecular evidence for new genera in the Afrotropical Cteninae (Araneae, Ctenidae) complex

Maximum parsimony and maximum likelihood analyses of the combined data sets of two chloroplast genes, rbcL and rps4, demonstrate that nk;the monotypic genus Gymnogrammitis is part of the polygrammoid clade (Polypodiaceae + Grammitidaceae), and not the Davalliaceae as proposed in most studies. The genus forms a clade together with two Asiatic genera of the Polypodiaceae, Arthromeris and Selliguea. These last two genera have either simple or once-pinnate leaves, whereas Gymnogrammitis has highly divided (3- to 4-pinnate) blades. Two characters of this genus, the basic chromosome number of x=36 and the absence of indusia, support a relationship with the Polypodiaceae. Neither feature is found within Davalliaceae. Three morphological characters support the placement of Gymnogrammitis within the selligueoid lineage of Polypodiaceae: spores with a thick perine extending in microspines, sclerenchymatous strands in the rhizome, and non-clathrate rhizome scales. These results demonstrate that molecular and morphological data are phylogenetically congruent with the exception of blade dissection. Our study clearly shows the pitfalls of classifications based on single characters, and illustrates the importance of phylogenetic assessment of all taxonomic conclusions.

BackgroundMatrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.ResultsWe systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.ConclusionsOur findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.