Phylogenomics in the Hard Pines (Pinus subsection Ponderosae; Pinaceae) Confirms Paraphyly in Pinus ponderosa, and Places Pinus jeffreyi with the California Big Cone Pines

2021 ◽  
Author(s):  
Ann Willyard ◽  
David S. Gernandt ◽  
Blake Cooper ◽  
Connor Douglas ◽  
Kristen Finch ◽  
...  
Keyword(s):  
Sierra Nevada ◽  
Pinus Ponderosa ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nucleotide Sequences ◽  
Nuclear Genes ◽  
Potential Zone ◽  
Species Trees ◽  
Pinus Jeffreyi ◽  
The Usa

We sampled 130 individuals (2 to 25 per taxon) of Pinus subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with Pinus subsect. Sabinianae based on morphological synapomorphiesas well as strong molecular phylogenetic support. Pinus ponderosa sensu lato is paraphyletic, and we suggest treatment as three species: P. ponderosa sensu stricto (with P. ponderosa var. ponderosa, P. ponderosa var. benthamiana, and P. ponderosa var. washoensis), P. scopulorum, and P. brachyptera. The persistence of lineages with the footprints of ancient nuclear introgression (labeled bpw in clade N4) and chloroplast capture (labeledbpw in clade P1) should caution species identification in Pinus subsection Ponderosae based on limited molecular data. The hybrid frequency was low based on cytonuclear discordance, and the persistence of an ancient P1 plastid clade is a better explanation than hybridization betweenP. ponderosa and P. jeffreyi for unexpected plastid associations in the western Sierra Nevada, USA. We identified a new potential zone of ancient admixture between P. ponderosa and P. scopulorum in Idaho, USA. Some populations of P. arizonica, P. brachyptera, P. engelmannii, and P. scopulorum in the USA are more closely related to taxa with distributions limited to Mexico than they are to each other. To integrate phylogeny and taxonomy, future work should sample widely in Mexico and the USA, score morphological characters (including seedling characters from the known seed parent), on the same individual as used for molecular data, and use methods that are based on individuals rather than population frequencies.

Reinstatement of Isotrema, a new generic delimitation of Aristolochia subgen. Siphisia (Aristolochiaceae)

Phytotaxa ◽  
2019 ◽  
Vol 401 (1) ◽  
pp. 1 ◽  
Author(s):  
XIN-XIN ZHU ◽  
XIAO-QIN LI ◽  
SHUAI LIAO ◽  
CHENG DU ◽  
YUAN WANG ◽  
...  
Keyword(s):  
South Asia ◽  
Central America ◽  
Outer Surface ◽  
Morphological Characters ◽  
Molecular Data ◽  
Comprehensive Analysis ◽  
Nuclear Genes ◽  
New Combinations ◽  
Generic Delimitation ◽  
Cladistic Analyses

Aristolochia subgen. Siphisia, comprising 98 species, is mainly distributed in East and South Asia, with some scattered in North and Central America. It has often been recognized as one of three subgenera of Aristolochia and can be distinguished from both remaining subgenera (Aristolochia subgen. Aristolochia and Aristolochia subgen. Pararistolochia) by morphological synapomorphies such as a strongly curved perianth with a 3-lobed limb, and especially the 3-lobed gynostemium, anthers paired on the outer surface of each gynostemium segment. However, recent cladistic analyses based on morphological characters and molecular data suggested that Aristolochia s.l. should be divided into four genera in two subtribes. In this study, a comprehensive analysis of molecular data of two plastid genic spacers (rps16-trnK and petB-petD), and two nuclear genes (phyA and ITS2) with an extensive sampling of Asian and American species was conducted. The combined datasets confirmed that Aristolochia subgen. Siphisia should be treated as an independent genus. Then Isotrema is reinstated here with 87 new combinations for the most comprehensive enumeration.

scholarly journals The Strepsiptera-Odyssey: the history of the systematic placement of an enigmatic parasitic insect order

Entomologia ◽  
2013 ◽  
pp. e4 ◽  
Author(s):  
H. Pohl ◽  
R.G. Beutel
Keyword(s):  
Single Copy ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Genes ◽  
Morphological Data ◽  
Data Sets ◽  
Protein Coding ◽  
Insect Order ◽  
Close Relationship ◽  
History Of

The history of the phylogenetic placement of the parasitic insect order Strepsiptera is outlined. The first species was described in 1793 by P. Rossi and assigned to the hymenopteran family Ichneumonidae. A position close to the cucujiform beetle family Rhipiphoridae was suggested by several earlier authors. Others proposed a close relationship with Diptera or even a group Pupariata including Diptera, Strepsiptera and Coccoidea. A subordinate placement within the polyphagan series Cucujiformia close to the wood-associated Lymexylidae was favored by the coleopterist R.A. Crowson. W. Hennig considered a sistergroup relationship with Coleoptera as the most likely hypothesis but emphasized the uncertainty. Cladistic analyses of morphological data sets yielded very different placements, alternatively as sistergroup of Coleoptera, Antliophora, or all other holometabolan orders. Results based on ribosomal genes suggested a sistergroup relationship with Diptera (Halteria concept). A clade Coleopterida (Strepsiptera and Coleoptera) was supported in two studies based on different combinations of protein coding nuclear genes. Analyses of data sets comprising seven or nine genes (7 single copy nuclear genes), respectively, yielded either a subordinate placement within Coleoptera or a sistergroup relationship with Neuropterida. Several early hypotheses based on a typological approach − affinities with Diptera, Coleoptera, a coleopteran subgroup, or Neuropterida − were revived using either a Hennigian approach or formal analyses of morphological characters or different molecular data sets. A phylogenomic approach finally supported a sistergroup relationship with monophyletic Coleoptera.

scholarly journals Integrative systematics untangles the evolutionary history of Stenochrus (Schizomida: Hubbardiidae), a neglected junkyard genus of North American short-tailed whipscorpions

2020 ◽  
Vol 130 (3) ◽  
pp. 458-479
Author(s):  
Rodrigo Monjaraz-Ruedas ◽  
Oscar F Francke ◽  
Lorenzo Prendini
Keyword(s):  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Present Contribution ◽  
Gene Markers ◽  
The Usa ◽  
Morphological And Molecular Data ◽  
Integrative Systematics

Abstract Until recently, the Nearctic short-tailed whipscorpion genus, StenochrusChamberlin, 1922, included 27 species distributed primarily in Mexico, the USA and Central America. Morphological disparity among its species, associated with their adaptation to diverse habitats, raised the question as to whether Stenochrus was monophyletic. The phylogenetic relationships among short-tailed whipscorpions have only recently begun to be explored, and the monophyly of Stenochrus had never been tested. The present contribution provides the first phylogeny of Stenochrus and related genera, based on 61 morphological characters and 2991 aligned DNA nucleotides from two nuclear and two mitochondrial gene markers, for 73 terminal taxa. Separate and simultaneous analyses of the morphological and molecular data sets were conducted with Bayesian Inference, Maximum Likelihood, and parsimony with equal and implied weighting. Terminals represented only by morphological data (‘orphans’) were included in some analyses for evaluation of their phylogenetic positions. As previously defined, Stenochrus sensuReddell & Cokendolpher (1991, 1995) was consistently polyphyletic and comprised eight monophyletic clades, justifying its reclassification into eight genera including Heteroschizomus Rowland, 1973, revalidated from synonymy with Stenochrus by Monjaraz-Ruedas et al. (2019). Rowland & Reddell’s (1980)mexicanus and pecki species groups were consistently paraphyletic. Orphans grouped with the most morphologically similar taxa.

Molecular and morphological evidence reveals three species within the California sister butterfly, Adelpha bredowii (Lepidoptera: Nymphalidae: Limenitidinae)

Zootaxa ◽  
2008 ◽  
Vol 1819 (1) ◽  
pp. 1 ◽  
Author(s):  
KATHLEEN L. PRUDIC ◽  
ANDREW D. WARREN ◽  
JORGE LLORENTE-BOUSQUETS
Keyword(s):  
Sequence Data ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Evidence ◽  
Reciprocal Monophyly ◽  
Southern Mexico ◽  
South Central ◽  
The Usa ◽  
Shared Alleles

In recent decades the butterfly Adelpha bredowii (Lepidoptera: Nymphalidae), known in the USA as the California Sister, has been considered to be a polytypic array of taxa, composed of two, three or four subspecies. The most recent review of the genus (Willmott 2003a) recognized three: A. b. bredowii, A. b. eulalia (= guatemalensis) and A. b. californica. We used mitochondrial (COII) and nuclear (Tpi) DNA sequence data, coupled with a reevaluation of traditional morphological characters, to determine the phylogenetic relationships between members of the A. bredowii complex, and to elucidate their taxonomic status. Phylogenetic analysis of molecular data corroborated the monophyly of each of the three subspecies (sensu Willmott), with the following topology: (bredowii + (eulalia + californica)). Average levels of COII variation among these taxa were much greater than the average variation within each taxon (3.4% vs. 0.2%, respectively). There were no shared alleles among these taxa, even from localities where two lineages (bredowii and eulalia) were collected in exact sympatry and synchrony. The degree of genetic divergence, reciprocal monophyly, and absence of shared alleles between taxa, coupled with unique morphological and distributional attributes of each, strongly suggest that A. bredowii, A. eulalia and A. californica are all species-level taxa, as they are treated herein (rev. stat.). Adelpha bredowii is endemic to western, central and southern Mexico: the syntype female (herein designated Lectotype) most likely originated near Oaxaca City, Oaxaca. Adelpha eulalia occurs from Guatemala, through much of Mexico, to Arizona, New Mexico and Texas, United States (as permanent residents; further north as vagrants), and occurs in exact sympatry with A. bredowii at least in Oaxaca, Mexico, but potentially in much of western and southwestern Mexico. The syntype female of eulalia (herein designated Lectotype) most likely originated from south-central Mexico. Adelpha californica is allopatric with respect to the other two species, occurring in northern Baja California, much of California, far western Nevada, Oregon and Washington. Our results highlight the continuous need for systematic scrutiny of familiar taxa, and raise the prospect that the genus Adelpha may be comprised of many more hidden species.

scholarly journals Diversity of Common Bean Landraces Collected in the Western and Eastern Carpatien

2011 ◽  
Vol 39 (No. 3) ◽  
pp. 73-83 ◽  
Author(s):  
O. Horňáková ◽  
M. Závodná ◽  
M. Žáková ◽  
J. Kraic ◽  
F. Debre
Keyword(s):  
Cluster Analysis ◽  
Common Bean ◽  
Morphological Characters ◽  
Molecular Data ◽  
Seed Traits ◽  
Phaseolus Vulgaris L ◽  
Growth Type ◽  
Banding Patterns ◽  
Polymorphism Detection ◽  
Thousand Seed Weight

The study of diversity in common bean was based on morphological and agronomical characteristics, differentiation of collected accessions by morphological and molecular markers, detection of genetic variation, and duplicates detection in bean landraces. The analysed 82 accessions of common bean (Phaseolus vulgaris L.) were collected in the Western andEastern Carpatien as landrace mixtures. Their seeds were segregated and pooled according to their characteristics; they were further multiplicated, and introduced into the collection. An extensive variation in plant and seed traits was discovered in thirty-three morphological and agronomical characteristics. Nevertheless, some of the accessions were identical in these characteristics. Cluster analysis grouped genotypes into two main branches, reflecting the growth type, seed size parameters, and thousand-seed weight. Molecular differentiation studies were performed by multilocus polymorphism detection in microsatellite and minisatellite DNA regions. Cluster analysis based on molecular data also grouped genotypes but no linkage to morphological traits was revealed. Bean accessions with very similar or identical morphological characters were clearly distinguished by DNA banding patterns. The presence of duplicates was excluded.  

scholarly journals Relicts from Glacial Times: The Ground Beetle Pterostichus adstrictus Eschscholtz, 1823 (Coleoptera: Carabidae) in the Austrian Alps

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 84
Author(s):  
Wolfgang Paill ◽  
Stephan Koblmüller ◽  
Thomas Friess ◽  
Barbara-Amina Gereben-Krenn ◽  
Christian Mairhuber ◽  
...  
Keyword(s):  
Ground Beetle ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Ice Age ◽  
Dispersal Ability ◽  
Austrian Alps ◽  
Alpine Regions ◽  
Extant Species ◽  
Limited Dispersal

The last ice age considerably influenced distribution patterns of extant species of plants and animals, with some of them now inhabiting disjunct areas in the subarctic/arctic and alpine regions. This arctic-alpine distribution is characteristic for many cold-adapted species with a limited dispersal ability and can be found in many invertebrate taxa, including ground beetles. The ground beetle Pterostichus adstrictus Eschscholtz, 1823 of the subgenus Bothriopterus was previously known to have a holarctic-circumpolar distribution, in Europe reaching its southern borders in Wales and southern Scandinavia. Here, we report the first findings of this species from the Austrian Ötztal Alps, representing also the southernmost edge of its currently known distribution, confirmed by the comparison of morphological characters to other Bothriopterus species and DNA barcoding data. Molecular data revealed a separation of the Austrian and Finish specimens with limited to no gene flow at all. Furthermore, we present the first data on habitat preference and seasonality of P. adstrictus in the Austrian Alps.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories

2020 ◽  
Vol 66 (3-4) ◽  
pp. 151-179
Author(s):  
L. Lee Grismer ◽  
L. Wood Perry ◽  
Marta S. Grismer ◽  
Evan S.H. Quah ◽  
Myint Kyaw Thura ◽  
...  
Keyword(s):  
Geographic Variation ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biodiversity Crisis ◽  
Allopatric Populations ◽  
Compelling Argument ◽  
Historical Accuracy ◽  
Molecular Phylogenetic

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

Post-fire survival and flushing in three Sierra Nevada conifers with high initial crown scorch

2009 ◽  
Vol 18 (7) ◽  
pp. 857 ◽  
Author(s):  
Chad T. Hanson ◽  
Malcolm P. North
Keyword(s):  
Sierra Nevada ◽  
Pinus Ponderosa ◽  
Fire Severity ◽  
Conifer Species ◽  
Mature Trees ◽  
Salvage Logging ◽  
Abies Magnifica ◽  
Crown Scorch ◽  
Tree Survival ◽  
Large Trees

With growing debate over the impacts of post-fire salvage logging in conifer forests of the western USA, managers need accurate assessments of tree survival when significant proportions of the crown have been scorched. The accuracy of fire severity measurements will be affected if trees that initially appear to be fire-killed prove to be viable after longer observation. Our goal was to quantify the extent to which three common Sierra Nevada conifer species may ‘flush’ (produce new foliage in the year following a fire from scorched portions of the crown) and survive after fire, and to identify tree or burn characteristics associated with survival. We found that, among ponderosa pines (Pinus ponderosa Dougl. ex. Laws) and Jeffrey pines (Pinus jeffreyi Grev. & Balf) with 100% initial crown scorch (no green foliage following the fire), the majority of mature trees flushed, and survived. Red fir (Abies magnifica A. Murr.) with high crown scorch (mean = 90%) also flushed, and most large trees survived. Our results indicate that, if flushing is not taken into account, fire severity assessments will tend to overestimate mortality and post-fire salvage could remove many large trees that appear dead but are not.

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