scholarly journals Phylogenetic placement of the enigmatic longhorned beetle Vesperoctenus flohri Bates (Vesperidae) and a first description of its female internal structures

2021 ◽  
Vol 79 ◽  
pp. 99-114
Author(s):  
Stephanie Haddad ◽  
Nayeli Gutiérrez ◽  
Felipe A. Noguera ◽  
Seunggwan Shin ◽  
Petr Svacha ◽  
...  
Keyword(s):  
Large Scale ◽  
Conservation Status ◽  
Mountain Range ◽  
Longhorned Beetle ◽  
Phylogenetic Significance ◽  
Phylogenetic Placement ◽  
Internal Structures ◽  
Statistical Support ◽  
Phylogenomic Analyses

Taxonomic placement of the enigmatic monotypic Mexican longhorned beetle genus Vesperoctenus Bates is examined through inclusion in and reanalysis of the dataset of Haddad et al. (2018, Systematic Entomology 43: 68–89). We describe and discuss the phylogenetic significance of the internal structures of a recently collected V. flohri female from the Sierra de la Laguna mountain range in Mexico, the same specimen from which phylogenomic data was generated. Our phylogenomic analyses (469 genes) recovered Vesperoctenus with maximal statistical support within the cerambyciform family Vesperidae, sister to Vesperus Dejean (Vesperinae). Vesperus + Vesperoctenus were recovered sister to Philinae, and collectively form a clade sister to Anoplodermatinae. Thus, we place V. flohri within Vesperidae: Vesperinae: Vesperoctenini based on analyses of large-scale phylogenomic data. Finally, we propose that the conservation status of V. flohri merits assessment.

scholarly journals Occurrence of the Green Shield-Moss Buxbaumia viridis (Moug.) Brid. in the Bieszczady Mountains of Poland

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 374
Author(s):  
Piotr Brewczyński ◽  
Kamil Grałek ◽  
Piotr Bilański
Keyword(s):  
National Park ◽  
Large Scale ◽  
Conservation Status ◽  
Natura 2000 ◽  
Field Work ◽  
Managed Forests ◽  
Moss Species ◽  
Microhabitat Preferences ◽  
Natura 2000 Site ◽  
Forest District

The small-sized gametophytes and sporophytes of the green shield-moss Buxbaumia viridis (Moug.) Brid. make it difficult to study. However, in Europe, there has been increasing interest in this species in the past few years, mostly as a result of the implementation of the Natura 2000 network. In Poland, B. viridis has only been reported in isolated studies that have been limited in terms of area and the number of participating workers. One of the Polish regions where B. viridis was recently recorded is the Bieszczady Mountains, but there have been no large-scale surveys of that region to date. The objective of the current work was to describe the B. viridis population in the Bieszczady Mountains in terms of its spatial distribution and abundance, investigate its selected microhabitat preferences, and evaluate the conservation status of this moss species within the Natura 2000 site Bieszczady PLC180001. The studied region encompassed 93,490.44 ha, including 69,056.23 ha of managed forests and 24,434.21 ha of forests belonging to the Bieszczady National Park. A preliminary survey was conducted in the Cisna Forest District (forest area of 19,555.82 ha) on 15–17 November 2017, while the main survey was performed in selected forest subcompartments of four forest districts—Baligród, Komańcza, Lutowiska, and Stuposiany—as well as the Bieszczady National Park from 5 to 16 November 2018. The field work consisted of searching for B. viridis sporophytes and setae and recording selected population and locality characteristics. The study led to the discovery of 353 new B. viridis localities in 202 study areas, with 9197 diploid individuals (sporophytes or setae only) growing in 545 microhabitats. The number of B. viridis localities discovered in the Bieszczady Mountains during 17 days of survey in 2017 and 2018 was two times higher than the combined number of localities previously found in Poland over more than 150 years (159 localities). Additionally, the number of sporophytes and setae identified was two times greater than their overall number in previous records. In addition, this study provides information about selected microhabitat preferences and the conservation status of this moss in the Bieszczady Natura 2000 site.

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

Fire history on a desert mountain range: Rincon Mountain Wilderness, Arizona, U.S.A.

1990 ◽  
Vol 20 (10) ◽  
pp. 1559-1569 ◽  
Author(s):  
Christopher H. Baisan ◽  
Thomas W. Swetnam
Keyword(s):  
Tree Ring ◽  
Large Scale ◽  
Fire History ◽  
Fire Regime ◽  
Forest Type ◽  
Drought Severity ◽  
Mountain Range ◽  
Mixed Conifer ◽  
The Mean ◽  
Mean Fire Interval

Modern fire records and fire-scarred remnant material collected from logs, snags, and stumps were used to reconstruct and analyze fire history in the mixed-conifer and pine forest above 2300 m within the Rincon Mountain Wilderness of Saguaro National Monument, Arizona, United States. Cross-dating of the remnant material allowed dating of fire events to the calendar year. Estimates of seasonal occurrence were compiled for larger fires. It was determined that the fire regime was dominated by large scale (> 200 ha), early-season (May–July) surface fires. The mean fire interval over the Mica Mountain study area for the period 1657–1893 was 6.1 years with a range of 1–13 years for larger fires. The mean fire interval for the mixed-conifer forest type (1748–1886) was 9.9 years with a range of 3–19 years. Thirty-five major fire years between 1700 and 1900 were compared with a tree-ring reconstruction of the Palmer drought severity index (PDSI). Mean July PDSI for 2 years prior to fires was higher (wetter) than average, while mean fire year PDSI was near average. This 490-year record of fire occurrence demonstrates the value of high-resolution (annual and seasonal) tree-ring analyses for documenting and interpreting temporal and spatial patterns of past fire regimes.

scholarly journals Reference genome assemblies reveal the origin and evolution of allohexaploid oat

2021 ◽  
Author(s):  
Yuanying Peng ◽  
Honghai Yan ◽  
Laichun Guo ◽  
Cao Deng ◽  
Lipeng Kang ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Higher Plants ◽  
Cereal Crops ◽  
Origin And Evolution ◽  
Avena Species ◽  
Oxford Nanopore ◽  
Reference Quality ◽  
Phylogenomic Analyses ◽  
Reference Genomes

Abstract Common oat (Avena sativa) is one of the most important cereal crops serving as a valuable source of forage and human food. While reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich, polyploid genome. By using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated the first reference-quality genome assembly of hulless common oat with a contig N50 of 93 Mb. We also assembled the genomes of diploid and tetraploid Avena ancestors, which enabled us to identify oat subgenome, large-scale structural rearrangements, and preferential gene loss in the C subgenome after hexaploidization. Phylogenomic analyses of cereal crops indicated that the oat lineage descended before wheat, offering oat as a unique window into the early evolution of polyploid plants. The origin and evolution of hexaploid oat is deduced from whole-genome sequencing, plastid genome and transcriptomes assemblies of numerous Avena species. The high-quality reference genomes of Avena species with different ploidies and the studies of their polyploidization history will facilitate the full use of crop gene resources and provide a reference for the molecular mechanisms underlying the polyploidization of higher plants, helping us to overcome food security challenges.

scholarly journals Mediterranean Summer Climate and the Importance of Middle East Topography*

2015 ◽  
Vol 28 (5) ◽  
pp. 1977-1996 ◽  
Author(s):  
Isla R. Simpson ◽  
Richard Seager ◽  
Tiffany A. Shaw ◽  
Mingfang Ting
Keyword(s):  
Middle East ◽  
Large Scale ◽  
Stationary Wave ◽  
Mountain Range ◽  
North African ◽  
Incident Flow ◽  
Low Level ◽  
Community Atmosphere Model ◽  
Moisture Deficit ◽  
The Mediterranean

Abstract In summer, the atmospheric circulation over the Mediterranean is characterized by localized intense subsidence and low-level northerlies over the central to eastern portion of the basin. Here, simulations with the Community Atmosphere Model, version 5 are used to investigate the influence of the elevated terrain of North Africa and the Middle East on this summertime circulation. This builds on previous work that recognized a role for North African topography in localizing the Mediterranean subsidence. By flattening the two regions of elevated terrain in the model, it is demonstrated that, while they both conspire to produce about 30% of the summertime subsidence, contrary to previous work, the mountains of the Middle East dominate in this topographic contribution by far. This topography, consisting primarily of the Zagros mountain range, alters the circulation throughout the depth of the troposphere over the Mediterranean and farther east. The model results suggest that about 20% of the Mediterranean summertime moisture deficit can be attributed to this mountain-induced circulation. This topography, therefore, plays an important role in the climate of the Mediterranean and the large-scale circulation over the rest of Eurasia during the summer. Further stationary wave modeling reveals that the mountain influence is produced via mechanical forcing of the flow. The greatest influence of the topography occurs when the low-level incident flow is easterly, as happens during the summer, primarily because of the presence of condensational heating over Asia. During other seasons, when the low-level incident flow is westerly, the influence of Middle East topography on the Mediterranean is negligible.

Iris pseudomeda (Iridaceae), a new species of Iris section Oncocyclus from Iran

Phytotaxa ◽  
2021 ◽  
Vol 527 (1) ◽  
pp. 75-82
Author(s):  
MONA SALIMBAHRAMI ◽  
HOJJATOLLAH SAEIDI ◽  
ALI BAGHERI
Keyword(s):  
New Species ◽  
Conservation Status ◽  
Distribution Range ◽  
Morphological Description ◽  
Mountain Range ◽  
Zagros Mountain ◽  
Taxonomic Relationships ◽  
Northwestern Iran ◽  
Botanical Illustrations ◽  
A New Species

Iris pseudomeda is described and illustrated as a new species of Iris section Oncocyclus from Kurdistan province in northwestern Iran. It occurs among subalpine flora of Zagros mountain range, on stony calcareous hillsides and the brink of grassland fields. A complete morphological description, conservation status, botanical illustrations, notes on habitat and distribution range are presented for the new species. Furthermore, taxonomic relationships of I. pseudomeda with other members of this rhizomatous bearded section, particularly I. meda, are also discussed.

scholarly journals Development of forest soils in the Krkonoše Mts. in the period 1980–2009

2010 ◽  
Vol 56 (No. 11) ◽  
pp. 485-504 ◽  
Author(s):  
K. Matějka ◽  
S. Vacek ◽  
V. Podrázský
Keyword(s):  
Species Composition ◽  
Tree Species ◽  
Large Scale ◽  
Vegetation Change ◽  
Soil Conditions ◽  
Available Phosphorus ◽  
Mountain Range ◽  
Site Conditions ◽  
Tree Species Composition ◽  
Spruce Stands

This paper documents the development of soil conditions in the set of 32 permanent research plots in the Krkonoše (Giant) Mts. These plots represent an altitudinal gradient covering the ecosystems of beech, mixed beech-spruce and spruce stands. In all plots, representing the site conditions of the highest areas of the mountain range, standard soil pits were prepared and the soil sampling was performed in autumn of years 1980, 1993, 1998, 2003 and 2009. The results reflect extreme site conditions, soil acidification, large scale surface liming and in minor extent also different tree species composition of the stands. The general type of the soil-genesis is represented by the podzolisation, overlapping the other soil-genetic factors, including the tree species composition. Nevertheless, this development is mostly expressed in the spruce stands. The beech dominance and/or co-dominance are reflected especially by more efficient N-cycling, higher pH, S and V values and fluctuation and lower extractable Al3+ content. More efficient cycling in beech ecosystems is insignificantly documented for plant available phosphorus, calcium and magnesium contents; on the contrary higher dynamics for iron ions was registered in the spruce stands. The long-term soil dynamics with a hysteresis (evident on the base of ordination analysis) can be divided into some periods – processes of acidification (typical in the 1980's samples), liming (main effect in 1993 and 1998) and regeneration (2003, 2009). Other features, important for the soil development, are probably related to the vegetation change, but this relation is not statistically significant.

scholarly journals The decline and conservation management of the threatened endemic palms of the Mascarene Islands

Oryx ◽  
2002 ◽  
Vol 36 (1) ◽  
pp. 56-65 ◽  
Author(s):  
Mike Maunder ◽  
Wayne Page ◽  
John Mauremootoo ◽  
Richard Payendee ◽  
Yousoof Mungroo ◽  
...  
Keyword(s):  
Large Scale ◽  
Conservation Management ◽  
Conservation Status ◽  
Iucn Red List ◽  
Ex Situ ◽  
Population Fragmentation ◽  
Wild Populations ◽  
Mascarene Islands

Abstract The conservation status of the five genera and 11 species of palm endemic to the Mascarene Islands (Mauritius, La Réunion and Rodriques) are reviewed. All species are threatened with extinction; nine taxa are classified as Critically Endangered and four as Endangered on the 2000 IUCN Red List. Two taxa survive as single wild specimens (Hyophorbe amaricaulis and Dictyosperma album var. conjugatum); an additional seven taxa have wild populations of 100 or fewer. Although the historical phase of large-scale forest clearance has passed, the remaining palm populations in the Mascarenes are under threat from the effects of population fragmentation, invasive plants and animals, and high levels of seed predation that prevent natural regeneration. The advantages of in situ management for the recovery of these palm populations are discussed. Without a long-term conservation programme, utilising both in situ and ex situ management, extinction of wild populations will occur.

scholarly journals Estimating the global conservation status of more than 15,000 Amazonian tree species

2015 ◽  
Vol 1 (10) ◽  
pp. e1500936 ◽  
Author(s):  
Hans ter Steege ◽  
Nigel C. A. Pitman ◽  
Timothy J. Killeen ◽  
William F. Laurance ◽  
Carlos A. Peres ◽  
...  
Keyword(s):  
Protected Areas ◽  
Tree Species ◽  
Large Scale ◽  
Gap Analysis ◽  
Extinction Risk ◽  
Conservation Status ◽  
Iucn Red List ◽  
Distribution Models ◽  
Threatened Plant Species ◽  
The Tropics

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world’s >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

scholarly journals Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Rei Kajitani ◽  
Dai Yoshimura ◽  
Yoshitoshi Ogura ◽  
Yasuhiro Gotoh ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
De Novo ◽  
Bacterial Genomes ◽  
Long Reads ◽  
Wide Range ◽  
Long Read ◽  
Phylogenomic Analyses ◽  
Error Removal ◽  
Iterative Error

Abstract De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

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