scholarly journals Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini)

ZooKeys ◽  
2020 ◽  
Vol 925 ◽  
pp. 1-54 ◽  
Author(s):  
Wayne P. Maddison ◽  
David R. Maddison ◽  
Shahan Derkarabetian ◽  
Marshal Hedin
Keyword(s):  
North America ◽  
Sex Chromosome ◽  
The Other ◽  
New Combinations ◽  
Rapid Radiation ◽  
Jumping Spiders ◽  
Neotropical Species ◽  
Genome Wide ◽  
A Genome ◽  
Senior Synonym

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribeAillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószyński, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola, A. sylvestris, A. cutleri, A. striatus, and A. finschi. The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 (A. dorsata, A. concolor, A. juniperi), (2) Tomis (T. welchi), and (3) Sittisax Prószyński, 2017 (S. ranieri). All Neotropical and Caribbean “Sitticus” are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus; the synonymy of Sitticus cabellensis Prószyński, 1971 with Pseudattulus kratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis. Six generic names are newly synonymized with Attulus and one with Attinella. Two Neotropical species are described as new, Jollas cupreussp. nov. and Tomis manabitasp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X1X2Y and X1X2X3Y), some of which (Sittisax ranieri and S. saxicola) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.

scholarly journals Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1606
Author(s):  
Shuai Zhang ◽  
Ruixue Wang ◽  
Cheng Huang ◽  
Ludan Zhang ◽  
Lin Sun
Keyword(s):  
Gene Expression ◽  
Sex Chromosome ◽  
Global Gene Expression ◽  
Regulatory Genes ◽  
Dosage Effect ◽  
Macromolecular Complex ◽  
Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Modulation Of Gene Expression

Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory genes were screened for an inverse dosage effect. Furthermore, we demonstrated that dosage changes of inverse regulator Inr-a/pcf11 can produce a genome-wide inverse dosage effect. All these findings suggest that the mechanism of genomic imbalance is related to the changes in the stoichiometric relationships of macromolecular complex members that affect the overall function. These studies may deepen the understanding of gene expression regulatory mechanisms.

scholarly journals Mitochondrial evidence supports a Nearctic origin for the spreading limicolous earthworm Sparganophilus tamesis Benham, 1892 (Clitellata, Sparganophilidae)

2016 ◽  
Vol 85 (1) ◽  
pp. 113-119 ◽  
Author(s):  
Emilia Rota ◽  
Svante Martinsson ◽  
Marco Bartoli ◽  
Anneke Beylich ◽  
Ulfert Graefe ◽  
...  
Keyword(s):  
North America ◽  
The Other ◽  
Distribution Area ◽  
Source Population ◽  
Widespread Species ◽  
Life Data ◽  
Senior Synonym ◽  
Morphological Diagnosis ◽  
European Haplotype ◽  
European Populations

We analysed samples of Sparganophilus taken at the corners of its distribution area in Europe (UK, Germany and Italy). No mitochondrial genetic divergence within and amongst them was found, neither in COI nor in 16S. Further, the COI haplotype was also identical to two sequences from Ontario, Canada in the Barcoding of Life Data System (BOLD) database. Our European COI and 16S sequences showed only minimal differentiation (only 1 or 2 substitutions) from specimens newly collected in Illinois and Washington states (USA), as well as from a COI haplotype from Tennessee (USA) in BOLD. An additional COI haplotype from Illinois (found in BOLD) is 2.1% different from the other haplotypes but clearly belongs to the same lineage of Sparganophilus . This geographically broad but genetically compact group fits the morphological diagnosis of S. tamesis Benham, 1892 as revised by Jamieson (1971) and is seen as evidence that all European populations 1) belong to the same species, 2) derive from a recent introduction, 3) are conspecific with the most widespread species of Sparganophilus in North America, and that 4) S. tamesis is a senior synonym of S. eiseni Smith, 1895. The single European haplotype does not refute the possibility of its spread from a single introduced source population.

scholarly journals Redescription and resolution of some Neotropical species of jumping spiders described by Caporiacco and description of a new species (Araneae: Salticidae)

2008 ◽  
Vol 25 (3) ◽  
pp. 487-494 ◽  
Author(s):  
Gustavo R. S. Ruiz ◽  
Antonio D. Brescovit
Keyword(s):  
New Species ◽  
French Guiana ◽  
Nominal Species ◽  
New Combinations ◽  
Type Specimens ◽  
Jumping Spiders ◽  
Neotropical Species ◽  
A New Species ◽  
Species Inquirendae

Type specimens of some of Caporiacco's Neotropical species are revised. The taxonomy of his species from French Guiana, whose type specimens are lost, is considered. The types of Corythalia hadzji Caporiacco, 1947, Corythalia luctuosa Caporiacco 1954, Hypaeus barromachadoi Caporiacco, 1947 and Naubolus melloleitaoi Caporiacco, 1947 are redescribed.The following new synonymies are established: Freya guianensis Caporiacco,1947 = Chira spinipes (Taczanowski, 1871) syn. nov.; Hypaeus bivittatus Caporiacco, 1947 = Hypaeus barromachadoi Caporiacco, 1947 syn. nov. New combinations are:Agelista petrusewiczi Caporiacco,1947 = Noegus petrusewiczi (Caporiacco,1947) comb. nov. .;Albionella chickeringi Caporiacco, 1954 = Mago chickeringi (Caporiacco,1954) comb. nov.;Asaracus pauciaculeis Caporiacco,1947 = Mago pauciaculeis (Caporiacco, 1947) comb. nov.; Cerionesta leucomystax Caporiacco, 1947 = Sassacus leucomystax (Caporiacco, 1947) comb. nov.; Lapsias guianensis Caporiacco, 1947 = Cobanus guianensis (Caporiacco, 1947) comb. nov.; Phiale modestissima Caporiacco, 1947 = Asaracus modestissimus (Caporiacco, 1947) comb. nov. The species Noegus lodovicoi sp. nov. is also described, based on an ex-syntype of Agelista petrusewiczi. The following nominal species are considered species inquirendae: Albionella guianensis Caporiacco, 1954, Alcmena trifasciata Caporiacco, 1954, Amycus effeminatus Caporiacco, 1954, Capidava variegata Caporiacco, 1954, Corythalia variegata Caporiacco, 1954, Dendryphantes coccineocinctus Caporiacco, 1954, Dendryphantes gertschi Caporiacco, 1947, Dendryphantes spinosissimus Caporiacco, 1954, Ilargus modestus Caporiacco, 1947, Lapsias melanopygus Caporiacco, 1947 = Frigga melanopygus (Caporiacco, 1947) comb. nov., Lurio splendidissimus Caporiacco, 1954, Nagaina modesta Caporiacco, 1954, Amycus patellaris (Caporiacco, 1954), Phidippus triangulifer Caporiacco, 1954 and Tutelina iridea Caporiacco, 1954.

scholarly journals A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

ZooKeys ◽  
2017 ◽  
Vol 695 ◽  
pp. 89-101 ◽  
Author(s):  
Wayne P. Maddison ◽  
Samuel C. Evans ◽  
Chris A. Hamilton ◽  
Jason E. Bond ◽  
Alan R. Lemmon ◽  
...  
Keyword(s):  
Jumping Spiders ◽  
Genome Wide ◽  
A Genome ◽  
Anchored Hybrid Enrichment

scholarly journals Modelling in molecular biology: describing transcription regulatory networks at different scales

2006 ◽  
Vol 361 (1467) ◽  
pp. 483-494 ◽  
Author(s):  
Thomas Schlitt ◽  
Alvis Brazma
Keyword(s):  
Regulatory Networks ◽  
Dynamic Models ◽  
Network Control ◽  
The Other ◽  
Control Logic ◽  
Functional Annotations ◽  
Genome Wide ◽  
A Genome ◽  
Finite State ◽  
Wide Scale

Approaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss the current state of the art for each of these approaches. We study the relationship between different topology models, and give examples how they can be used to infer functional annotations for genes of unknown function. We introduce a new simple way of describing dynamic models called finite state linear model (FSLM). We discuss the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact.

scholarly journals The genomics of rapid climatic adaptation and parallel evolution in North American house mice

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009495
Author(s):  
Kathleen G. Ferris ◽  
Andreas S. Chavez ◽  
Taichi A. Suzuki ◽  
Elizabeth J. Beckman ◽  
Megan Phifer-Rixey ◽  
...  
Keyword(s):  
Body Weight ◽  
North America ◽  
Genome Wide Association Study ◽  
Phenotypic Change ◽  
House Mice ◽  
Western North America ◽  
Selection Pressures ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.

scholarly journals Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sherry Lou Hechanova ◽  
Kamal Bhattarai ◽  
Eliza Vie Simon ◽  
Graciana Clave ◽  
Pathmasiri Karunarathne ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
The Other ◽  
Sequence Alignments ◽  
Rice Varieties ◽  
Genome Species ◽  
Genome Wide ◽  
Wild Rice Species ◽  
A Genome ◽  
Aa Genome

AbstractWild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.

scholarly journals Cladid crinoids from the Late Kinderhookian Meadville Shale, Cuyahoga Formation of Ohio

2012 ◽  
Vol 86 (3) ◽  
pp. 470-487 ◽  
Author(s):  
Thomas W. Kammer ◽  
Edgar W. Roeser
Keyword(s):  
New Species ◽  
North America ◽  
New Taxa ◽  
Endemic Species ◽  
New Genus ◽  
New Combinations ◽  
New Genus And Species ◽  
Rapid Radiation

A total of 17 species of cladid crinoids are documented from the late Kinderhookian Meadville Shale Member of the Cuyahoga Formation of northeastern Ohio, the most diverse assemblage of Kinderhookian-age cladids known in North America. One new genus, six new species, and seven new combinations are reported. New taxa include Cuyahogacrinus lodiensis new genus and species, and the new species Cyathocrinites simplex, Atelestocrinus meszarosi, Goniocrinus sceletus, Aphelecrinus gracilis, and Lebetocrinus ohioensis. New combinations include Logocrinus warreni (Laudon et al., 1952), Histocrinus aegina (Hall, 1863), Paracosmetocrinus richfieldensis (Worthen, 1882), P. corycia (Hall, 1863), Acylocrinus lyriope (Hall, 1863), Linocrinus merope (Hall, 1863), and L. paternus (Hall, 1863). Remaining taxa include Cyathocrinites lamellosus (White, 1863) and Ascetocrinus whitei (Hall, 1861), both of which also occur in the Osagean Burlington Limestone, and the endemic species Cosmetocrinus crineus (Hall, 1863) and Pachylocrinus subtortuosus (Hall, 1863).Collectively, the cosmopolitan genera and species of cladids show a greater overall affinity with Osagean cladid faunas than with other Kinderhookian cladid faunas. However, this is true for other Kinderhookian cladid faunas as well that individually have more taxa in common with Osagean faunas than other Kinderhookian faunas. This suggests a greater degree of endemism and local speciation during the Kinderhookian as a prelude to the rapid radiation of cladids, and other crinoids, during the Osagean.

scholarly journals On the taxonomy of some neotropical species of jumping spiders described by Caporiacco (Araneae, Salticidae)

2007 ◽  
Vol 24 (2) ◽  
pp. 376-381 ◽  
Author(s):  
Gustavo R.S. Ruiz ◽  
Antonio D. Brescovit ◽  
Arno A. Lise
Keyword(s):  
Type Species ◽  
New Combinations ◽  
Jumping Spiders ◽  
Neotropical Species

Pseudattulus incertus Caporiacco, 1955 is synonymized with P. kratochvili Caporiacco, 1947 and the male of this species is redescribed. The genus Uspachus Galiano, 1995 is synonymized with Romitia Caporiacco, 1947 and the male of its type species, R. nigra Caporiacco, 1947, is redescribed. The following new combinations are established for the species formerly included in Uspachus: Romitia albipalpis (Taczanowski, 1878), Romitia andina (Taczanowski, 1878), Romitia bahiensis (Galiano, 1995), Romitia colombiana (Galiano, 1995), Romitia juquiaensis (Galiano, 1995), Romitia ministerialis (C.L. Koch, 1846), Romitia misionensis (Galiano, 1995) and Romitia patellaris (Galiano, 1995). The genus Pseudamphidraus Caporiacco, 1947 is synonymized with Noegus Simon, 1900 by transfer of its type species, Noegus niger (Caporiacco, 1947) comb. nov., whose male is herein redescribed. The species Pseudamphidraus variegatus Caporiacco, 1947 and Marma trifidocarinata Caporiacco, 1947 are synonymized with Marma nigritarsis (Simon, 1900).

scholarly journals A general model to explain repeated turnovers of sex determination in the Salicaceae

2020 ◽  
Author(s):  
Wenlu Yang ◽  
Zhiyang Zhang ◽  
Deyan Wang ◽  
Yiling Li ◽  
Shaofei Tong ◽  
...  
Keyword(s):  
Sex Determination ◽  
General Model ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Response Regulator ◽  
Single Gene ◽  
Entire Family ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome

AbstractDioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosome in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

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