scholarly journals Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

2021 ◽  
Author(s):  
Jessie F Salter ◽  
Peter A Hosner ◽  
Edward L Braun ◽  
Rebecca T Kimball ◽  
Robb T Brumfield ◽  
...  
Keyword(s):  
New World ◽  
Phylogenetic Analyses ◽  
Species Level ◽  
Phylogenetic Structure ◽  
Northern Bobwhites ◽  
Geographic Structure ◽  
Subspecies Level ◽  
History Of ◽  
Diverse Groups ◽  
Historical Samples

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.

Molecular Phylogeny of the Notomicrine Water Beetles (Coleoptera: Noteridae) Reveals Signatures of Gondwanan Vicariance and Ecological Plasticity

2020 ◽  
Vol 4 (6) ◽  
Author(s):  
Stephen M Baca ◽  
Andrew E Z Short
Keyword(s):  
New World ◽  
Mitochondrial Gene ◽  
Species Level ◽  
Divergence Times ◽  
Undescribed Species ◽  
Water Beetles ◽  
Old World ◽  
Ecological Plasticity ◽  
History Of ◽  
Species Groups

Abstract Notomicrinae (Coleoptera: Noteridae) is a subfamily of minute and ecologically diverse aquatic beetles distributed across the Southeast Asia, Oceania, and the Americas. We investigate the evolution of Notomicrinae and construct the first species-level phylogeny within Noteridae using five nuclear and mitochondrial gene fragments. We focus on the genus Notomicrus Sharp (Coleoptera: Noteridae), sampling 13 of the 17 known Notomicrus species and an additional 11 putative undescribed species. We also include Phreatodytes haibaraensis Uéno (Coleoptera: Noteridae). Datasets are analyzed in Maximum Likelihood and Bayesian frameworks. With these, we 1) estimate divergence times among notomicrine taxa and reconstruct the biogeographical history of the group, particularly testing the hypothesis of Gondwanan vicariance between Old World and New World Notomicrus; 2) additionally, we assess ecological plasticity within Notomicrinae in the context of the phylogeny; and 3) finally, we test the monophyly of tentative species groups within Notomicrus and place putative new taxa. We recover a monophyletic Notomicrinae, with Phreatodytes sister to Notomicrus. We estimate the crown age of Notomicrinae to be ca. 110 Mya. The crown age of Notomicrus is recovered as ca. 75 Mya, there diverging into reciprocally monophyletic Old and New World clades, suggesting Gondwanan vicariance. Our phylogenetic estimate indicates a strong degree of ecological plasticity within Notomicrinae, with habitat switching occurring in recently diverging taxa. Finally, we recover five main species groups in Notomicrus, one Old World, Four New World, with tentative affirmation of the placement of undescribed species.

Plastome and Nuclear Phylogenies of Dwarf Mistletoes (Arceuthobium: Viscaceae)

2021 ◽  
Vol 46 (2) ◽  
pp. 389-402
Author(s):  
Adam C. Schneider ◽  
Kate M. Sanders ◽  
Jacob H. Idec ◽  
Yun Jee Lee ◽  
Shawn C. Kenaley ◽  
...  
Keyword(s):  
New World ◽  
Sequence Data ◽  
Strong Support ◽  
Species Level ◽  
Species Relationships ◽  
Plastome Evolution ◽  
Subspecies Level ◽  
Infraspecific Taxa ◽  
Ribosomal Cistron ◽  
Number Of Individuals

Abstract— Dwarf mistletoes are a lineage of morphologically-reduced stem parasites inhabiting Pinaceae and Cupressaceae throughout the northern hemisphere and equatorial East Africa. Though diagnosable by a suite of morphological traits, phylogenetic knowledge of species relationships has been limited to studies employing either comprehensive taxonomic sampling of one or two genes, or more sequence data from a limited number of individuals. We used data from genome skimming to assemble 3kb of the nuclear ribosomal cistron and up to 45kb of the plastome to clarify the phylogenetic root of the genus, monophyly of species, and relationships among infraspecific taxa. Genomic differentiation among terminal taxa was variable; however, we found strong support for reciprocally monophyletic New World and Old World lineages, congruent nrDNA and plastome topologies at the species level and below, and monophyly of most taxonomic sections and species. Plastome gene content was stable across the genus with minimal pseudogenization or loss, as in other hemiparasites, with the notable exception of cemA. These findings form the basis of our re-evaluation of historical biogeographical hypotheses, species- and subspecies-level taxonomy, and plastome evolution in Arceuthobium. More broadly, this work provides a foundation for future clade-focused comparative and biosystematics studies of Arceuthobium.

The trouble with trilobites: classification, phylogeny and the cryptogenesis problem

2019 ◽  
Vol 157 (1) ◽  
pp. 35-46 ◽  
Author(s):  
John R. Paterson
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Species Level ◽  
Intensive Study ◽  
Future Directions ◽  
History Of ◽  
Cambrian Trilobite ◽  
Taxonomic Studies ◽  
Broad Scale

AbstractTrilobites are an iconic group of extinct arthropods that lived in Palaeozoic oceans for c. 270 Ma, before their demise at the end of the Permian Period. Despite their considerable diversity (> 22 000 species) and abundance, particularly in Cambrian and Ordovician rocks, as well as intensive study for well over 200 years, trilobite systematics remains in a state of flux. In this contribution, the complex history of trilobite classification over the last century is briefly reviewed, including the seminal scheme published by Henry Swinnerton in 1915. The cryptogenesis problem, which relates to the supposedly obscure phylogenetic links between major post-Cambrian trilobite clades and their Cambrian sister taxa, is also discussed. Previous studies have suggested that the cryptogenesis problem is largely a taxonomic artefact, but the Cambrian origins of some post-Cambrian groups, such as the orders Proetida and Odontopleurida, are still unclear. Future directions for research on trilobite systematics are outlined, from taxonomic studies involving comprehensive documentation and extensive illustration of morphology at the species level, through to broad-scale phylogenetic analyses that initiate or test hypotheses about relationships across the major groups. Other ongoing issues to be addressed include identifying the sister group of Trilobita, and determining whether certain taxa, such as the suborder Agnostina and Cambrian family Burlingiidae, represent trilobites.

Perizomini (Lepidoptera: Geometridae: Larentiinae) are polyphyletic

2020 ◽  
Vol 51 (3) ◽  
pp. 489-516
Author(s):  
Erki Õunap ◽  
Toomas Tammaru ◽  
Andro Truuverk
Keyword(s):  
Maximum Likelihood ◽  
Molecular Systematics ◽  
New World ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Morphological Evidence ◽  
Worldwide Distribution ◽  
The Family ◽  
History Of ◽  
Open Question

Recent advances in molecular systematics have led to an emerging understanding of the phylogenetic history of the family Geometridae. These studies have basically confirmed the traditional subdivision of the subfamily Larentiinae into tribes but unsolved problems remain. Here we test the monophyly of the tribe Perizomini, and evaluate the division of this tribe into genera using Bayesian and maximum likelihood analyses of one mitochondrial and eight nuclear gene fragments. We show that the Eurasian members of Perizoma Hübner, 1825, Mesotype Hübner, 1825 and Gagitodes Warren, 1893 together form a monophyetic tribe Perizomini. However, Martania Mironov, 2000 is not closely related to these genera, but is considered to belong to Melanthiini according to the results of the phylogenetic analyses. Morphological evidence supporting this rearrangement is discussed. The Nearctic Larentia basaliata Walker, 1862 was shown to belong in the genus Martania as M. basaliata (Walker, 1862) comb. nov. and being specifically distinct from the morphologically similar Palaearctic M. taeniata. Three other studied ‘Perizoma’ species from the New World were similarly placed far from Perizomini in the phylogenetic tree, and were not related to each other. We conclude that both the tribe Perizomini and the genus Perizoma are polyphyletic which indicates that the group needs a global revision. It remains an open question whether Perizomini have a worldwide distribution as previously assumed, or is this tribe confined to the Palaearctic region.

scholarly journals Phylogeography of the ‘cosmopolitan’ orb-weaver Argiope trifasciata (Araneae: Araneidae)

2020 ◽  
Vol 131 (1) ◽  
pp. 61-75
Author(s):  
Christoph Abel ◽  
Jutta M Schneider ◽  
Matjaž Kuntner ◽  
Danilo Harms
Keyword(s):  
Species Delimitation ◽  
Evolutionary History ◽  
New World ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Spider Species ◽  
Evolutionary Origins ◽  
History Of ◽  
Argiope Trifasciata ◽  
Species Taxonomy

Abstract Few spider species show truly cosmopolitan distributions. Among them is the banded garden spider Argiope trifasciata, which is reported from six continents across major climatic gradients and geographical boundaries. In orb-weaver spiders, such global distributions might be a result of lively dispersal via ballooning. However, wide distributions might also be artefactual, owing to our limited understanding of species taxonomy. To test the hypothesis that A. trifasciata might be a complex of cryptic species with more limited geographical ranges, we investigated the biogeographical structure and evolutionary history of A. trifasciata through a combination of time-calibrated phylogenetic analyses (57 terminals and three genes), ancestral range reconstruction and species delimitation methods. Our results strongly suggest that A. trifasciata as currently defined is not a single species. Its populations fall into five reciprocally monophyletic clades that are genetically distinct and have evolutionary origins in the Plio-Pleistocene. These clades are confined to East Asia, temperate Australia, Hawaii, the New World and the Old World (Africa and most of the Palaearctic). Our results provide the basis for future investigation of morphological and/or ecological disparity between the populations that are likely to represent species, in addition to examinations of the attributes and dispersal modes of these species.

scholarly journals TAXONOMIC COMPOSITION OF THE Rhabdophis subminiatus (SCHLEGEL, 1837) SPECIES COMPLEX (REPTILIA: NATRICIDAE) WITH THE DESCRIPTION OF A NEW SPECIES FROM CHINA

2021 ◽  
Vol 10 (2) ◽  
pp. 89-120
Author(s):  
Patrick David ◽  
Gernot Vogel
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Hainan Island ◽  
Morphological Characters ◽  
Taxonomic Composition ◽  
Species Level ◽  
Subspecies Level ◽  
Definition Of ◽  
A New Species

The systematics of Rhabdophis subminiatus (Schlegel, 1837) at subspecies level has long proved to be controversial. We analyse the variation of selected morphological characters in 179 specimens from populations covering the whole range of R. subminiatus sensu lato. Based on this review, we recognize four morphological groups, of which two do not agree with the current definitions and distributions of the currently recognized subspecies R. s. subminiatus. The “northernmost group” agrees with the definition of Natrix helleri Schmidt, 1925. In contrast, the “southernmost group” agrees with the syntypes of Tropidonotus subminiatus and we here restrict this species to the Sunda Region. We also discuss a previous designation of the lectotype of T. subminiatus, which we consider invalid, and we here make it valid in the sense of the Code. Furthermore, our analysis allows us to define a third group that is widespread in the Indochinese Region and Malayan Peninsula. For this geographically “central group”, the name Natrix subminiata siamensis Mell, 1931, is available. We therefore resurrect this taxon from its synonymy with R. subminiatus and we designate a lectotype in agreement with requirements of the Code. Lastly, we recognize a fourth group at species level, endemic to Hainan Island, China, that we describe as a new species. This division into four morphological groups at species level is coherent with phylogenetic analyses recently published in the literature. We also discuss and modify the taxonomic status of Natrix subminiata hongkongensis Mell, 1931 and Natrix (Rhabdophis) laobaoensis Bourret, 1934, now regarded as synonyms of R. subminiatus and R. siamensis, respectively.

Ethics of Conducting Virtual Ethnography on Visual Platforms

2018 ◽  
Vol 12 (2) ◽  
pp. 163-178
Author(s):  
Kayla Wheeler
Keyword(s):  
African American ◽  
Online Community ◽  
Gender Segregation ◽  
Religious Groups ◽  
Virtual Ethnography ◽  
History Of ◽  
Standard Set ◽  
Potential Risks ◽  
Visually Based ◽  
Diverse Groups

For scholars, the internet provides a space to study diverse groups of people across the world and can be a useful way to bypass physical gender segregation and travel constraints. Despite the potential for new insights into people’s everyday life and increased attention from scholars, there is no standard set of ethics for conducting virtual ethnography on visually based platforms, like YouTube and Instagram. While publicly accessible social media posts are often understood to be a part of the public domain and thus do not require a researcher to obtain a user’s consent before publishing data, caution must be taken when studying members of a vulnerable community, especially those who have a history of surveillance, like African-American Muslims. Using a womanist approach, the author provides recommendations for studying vulnerable religious groups online, based on a case study of a YouTube channel, Muslimah2Muslimah, operated by two African-American Muslim women. The article provides an important contribution to the field of media studies because the author discusses a “dead” online community, where users no longer comment on the videos and do not maintain their own profiles, making obtaining consent difficult and the potential risks of revealing information to an unknown community hard to gauge.

Scriptural Battlefields: The Old Testament, Legal Culture, and the Polemics of the Spanish New World Empire, 1492–1821

2019 ◽  
Author(s):  
Jorge Cañizares-Esguerra ◽  
Adrian Masters
Keyword(s):  
Old Testament ◽  
Social Order ◽  
New World ◽  
Legal Culture ◽  
Spanish Empire ◽  
Correct Interpretation ◽  
Group Status ◽  
History Of ◽  
New Social Order

Scholars have barely begun to explore the role of the Old Testament in the history of the Spanish New World. And yet this text was central for the Empire’s legal thought, playing a role in its legislation, adjudication, and understandings of group status. Institutions like the Council of the Indies, the Inquisition, and the monarchy itself invited countless parallels to ancient Hebrew justice. Scripture influenced how subjects understood and valued imperial space as well as theories about Paradise or King Solomon’s mines of Ophir. Scripture shaped debates about the nature of the New World past, the legitimacy of the conquest, and the questions of mining, taxation, and other major issues. In the world of privilege and status, conquerors and pessimists could depict the New World and its peoples as the antithesis of Israel and the Israelites, while activists, patriots, and women flipped the script with aplomb. In the readings of Indians, American-born Spaniards, nuns, and others, the correct interpretation of the Old Testament justified a new social order where these groups’ supposed demerits were in reality their virtues. Indeed, vassals and royal officials’ interpretations of the Old Testament are as diverse as the Spanish Empire itself. Scripture even outlasted the Empire. As republicans defeated royalists in the nineteenth century, divergent readings of the book, variously supporting the Israelite monarchy or the Hebrew republic, had their day on the battlefield itself.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Molecular Analysis of Targeted Insecticide Resistance Gene Mutations in Field-Caught Mosquitos of Medical Importance From Saudi Arabia

2021 ◽  
Author(s):  
Yuan Fang ◽  
Ernest Tambo ◽  
Jing-Bo Xue ◽  
Yi Zhang ◽  
Xiao-Nong Zhou ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Insecticide Resistance ◽  
Resistance Gene ◽  
Phylogenetic Analyses ◽  
Gene Mutations ◽  
Mosquito Vector ◽  
Dengue Disease ◽  
The Status ◽  
History Of ◽  
Exon 20

Abstract Gene mutations on target sites can be a valuable indicator of the status of insecticide resistance. Jeddah, a global commercial and major port-of-entry city, is bearing the brunt of dengue disease burden in Saudi Arabia. In the current study, six genotypes of three codon combinations (989, 1016, and 1534) were observed on voltage-gated sodium channel (VGSC) gene in Jeddah’s Aedes aegypti population, with PGF/PGC as the dominant one. Two types of introns between exon 20 and 21 on VGSC have been identified for the first time in Ae. aegypti in Saudi Arabia. Statistical and phylogenetic analyses showed that the intron type was significantly associated with the 1016 allele and may reflect the history of insecticide treatment in different continents. In addition, fixation of the L1014F allele on VGSC and G119S on acetylcholinesterase 1 gene was detected in local Culex quinquefasciatus populations, with frequencies of 95.24 and 100%, respectively. To the best of our knowledge, this is the first report of resistant-associated mutations in field-caught Cx. quinquefasciatus in Saudi Arabia. The high prevalence of insecticide resistance gene mutations in local primary mosquito vector species highlights the urgent need to carry out comprehensive insecticide resistance surveillance in Saudi Arabia.

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