Complex patterns of chromosomal variation along a latitudinal cline in the grasshopper Caledia captiva

Genome ◽  
1988 ◽  
Vol 30 (2) ◽  
pp. 108-117 ◽  
Author(s):  
David D. Shaw ◽  
David J. Coates ◽  
Michael L. Arnold
Keyword(s):  
Dna Sequences ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Allozyme Variation ◽  
Latitudinal Cline ◽  
Chromosomal Variation ◽  
Genomic Change ◽  
Southern Limit ◽  
The North ◽  
Complex Patterns

An analysis of chromosomal variation along a 1500-km latitudinal cline in the Moreton subspecies of Caledia captiva has revealed the existence of complex and systemic changes to genome structure. These changes involved variation in the position of the centromere on every chromosome, from medial locations in northern populations to more distal or terminal locations in the southern populations. At the ends of this genomic cline, two contrasting chromosomal patterns were evident. In the north, the genome was fixed for metacentric chromosomes whereas at the southern limit, the genome was homozygous for acrocentric and telocentric chromosomes. Intermediate populations showed highly complex patterns of chromosomal polymorphisms. All populations along the cline were homogeneous for mitochondrial DNA restriction fragment length polymorphisms, highly repeated DNA sequences, and allozyme variation, with no evidence of genetic differentiation or inhibition of gene flow. It is argued that these complex patterns of genomic change reveal evidence of an adaptive role for both fixed and polymorphic chromosomal rearrangements within the same taxon.Key words: chromosome variation, natural selection, Caledia, grasshopper.

scholarly journals Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

2021 ◽  
Author(s):  
James D. Galbraith ◽  
R. Daniel Kortschak ◽  
Alexander Suh ◽  
David L. Adelson
Keyword(s):  
Transposable Elements ◽  
Zebra Finch ◽  
Dna Sequences ◽  
Genome Stability ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Past Research ◽  
Dominant Group ◽  
Avian Genome ◽  
Retrotransposon Activity

AbstractSince the sequencing of the zebra finch genome it has become clear the avian genome, while largely stable in terms of chromosome number and gene synteny, is more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element content have been noted across the avian tree. Transposable elements (TEs) are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through non-allelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, CR1 retrotransposons, either focusing on their expansion within single orders, or comparing passerines to non-passerines. Here we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and with orders. We describe high levels of TE expansion in genera which have speciated in the last 10 million years including kiwis, geese and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals.Author SummaryTransposable elements (TEs) are mobile, self replicating DNA sequences within a species’ genome, and are ubiquitous sources of mutation. The dominant group of TEs within birds are chicken repeat 1 (CR1) retrotransposons, making up 7-10% of the typical avian genome. Because past research has examined the recent inactivity of CR1s within model birds such as the chicken and the zebra finch, this has fostered an erroneous view that all birds have low or no TE activity on recent timescales. Our analysis of numerous high quality avian genomes across multiple orders identified both similarities and significant differences in how CR1s expanded. Our results challenge the established view that TEs in birds are largely inactive and instead suggest that their variation in recent activity may contribute to lineage-specific changes in genome structure. Many of the patterns we identify in birds have previously been seen in mammals, highlighting parallels between the evolution of birds and mammals.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

scholarly journals The M26 Hotspot of Schizosaccharomyces pombe Stimulates Meiotic Ectopic Recombination and Chromosomal Rearrangements

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1191-1204 ◽  
Author(s):  
Jeffrey B Virgin ◽  
Jeffrey P Bailey
Keyword(s):  
Homologous Recombination ◽  
Schizosaccharomyces Pombe ◽  
Dna Sequences ◽  
Chromosomal Rearrangements ◽  
Low Frequency ◽  
Repeated Sequences ◽  
Crossing Over ◽  
Ectopic Recombination ◽  
Recombination Hotspots ◽  
Integration Sites

Abstract Homologous recombination is increased during meiosis between DNA sequences at the same chromosomal position (allelic recombination) and at different chromosomal positions (ectopic recombination). Recombination hotspots are important elements in controlling meiotic allelic recombination. We have used artificially dispersed copies of the ade6 gene in Schizosaccharomyces pombe to study hotspot activity in meiotic ectopic recombination. Ectopic recombination was reduced 10–1000-fold relative to allelic recombination, and was similar to the low frequency of ectopic recombination between naturally repeated sequences in S. pombe. The M26 hotspot was active in ectopic recombination in some, but not all, integration sites, with the same pattern of activity and inactivity in ectopic and allelic recombination. Crossing over in ectopic recombination, resulting in chromosomal rearrangements, was associated with 35–60% of recombination events and was stimulated 12-fold by M26. These results suggest overlap in the mechanisms of ectopic and allelic recombination and indicate that hotspots can stimulate chromosomal rearrangements.

Environmental and Genetic Control of Reproduction in Danthonia caespitosa Populations

1978 ◽  
Vol 26 (3) ◽  
pp. 351 ◽  
Author(s):  
KC Hodgkinson ◽  
JA Quinn
Keyword(s):  
Floral Induction ◽  
Flag Leaf ◽  
Day Length ◽  
Herbarium Specimens ◽  
Floral Initiation ◽  
Inflorescence Development ◽  
Southern Limit ◽  
The North ◽  
Eastern Australia ◽  
Controlled Environments

Seedlings and older plants of five populations of Danthonia caespitosa from south-eastern Australia were grown in controlled environments and in a transplant garden to determine the effect of day length, temperature, and vernalization of floral initiation and inflorescence development. The populations were selected from widely separated sites which spanned the latitudinal range (31-42°S.) for the species and extended from a hot, semiarid environment in the north to a relatively cool and moist temperature environment in the south. Examination of herbarium specimens indicated that seed set could occur as early as mid September at the northern limit for the species and not before mid January at the southern limit (Tasmania). In a uniform transplant garden located at Deniliquin (latitude 35° 23′S.) plants from the northern site reached anthesis 4 weeks earlier than plants from southern sites. Controlled environment experiments revealed that D. caespitosa is a long-day plant. Northern populations required a 9 . 5 hr day length or longer for floral induction compared with 11 hr or longer for southern populations. The number of days in inductive conditions (outside, day length 13.5 hr) required for floral initiation was 5-7 for the three most northern populations and 21-25 days for the two southern populations. Inflorescence development (initiation to flag leaf stage) was considerably slower in southern populations. All but the most northern population responded to vernalization. Flowering was earlier in temperatures that were optimal for plant growth. At high temperatures (36/31°C day/night) flowering was not significantly delayed for the three most northern populations, but was for the two southern populations, and florets contained caryopses in only the three northern populations. These results suggest that in cool and moist temperate habitats reproduction of this species is programmed by day length and temperature effects on floral initiation and development to coincide with a predictable growing season, whereas in hot semiarid habitats this control is relaxed, which permits opportunistic reproduction whenever soil moisture and temperature permit growth.

Le synclinal danien-eocene de La Mourotte (Var)

1962 ◽  
Vol S7-IV (1) ◽  
pp. 87-91 ◽  
Author(s):  
Fernand Touraine
Keyword(s):  
Upper Jurassic ◽  
The South ◽  
Northern Limit ◽  
Southern Limit ◽  
The North ◽  
Bird Eggs ◽  
Tectonic Study ◽  
Dinosaur Eggs

Abstract Results of a stratigraphic and tectonic study of the Mourotte syncline, Provence, France, divide the structure into three parts. The northern part is composed of Hauterivian littoral beds containing Danian dinosaur eggs. The Danian limestone-sandstone series disappears at La Neuve while the marly upper Danian beds continue to the extreme northern limit of the syncline. In the central part the Hauterivian wedges out, and toward its southern limit the substratum is entirely upper Jurassic. In the southern part, the Danian limestones are only visible on the northeast border. Bird eggs collected in the area assign the southern part of the syncline to the Thanetian. Overturning is less noticeable in the north, becoming acute toward the south where the syncline is tightly overturned.

The reproductive biology and ecology of Gammarus duebeni (Crustacea: Amphipoda) in southern England

1983 ◽  
Vol 63 (3) ◽  
pp. 517-540 ◽  
Author(s):  
Martin Sheader
Keyword(s):  
Life Cycle ◽  
Egg Production ◽  
Breeding Strategy ◽  
Female Size ◽  
Temperature Dependent ◽  
Southern Limit ◽  
Factors Affecting ◽  
North East ◽  
The North ◽  
Test Estuary

A study was made of the life cycle and reproductive ecology of Gammarus duebeni in the Test Estuary on the south coast of England. The species is towards the southern limit of its distributional range in the north-east Atlantic, which results in breeding continuing throughout much of the year. The breeding strategy employed was found to vary with season. The size of eggs produced and the rate of egg production were both temperature dependent, whereas the proportion of production expended on eggs and the number of eggs per brood, although probably influenced by temperature appeared to be controlled by food availability and female size. Factors affecting the mortality of eggs within the marsupium and breeding synchrony were considered in relation to season. The life cycle consisted of two major overlapping generations.

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 62 (1) ◽  
pp. 427-446 ◽  
Author(s):  
Susana Schönhuth ◽  
David M. Hillis ◽  
David A. Neely ◽  
Lourdes Lozano-Vilano ◽  
Anabel Perdices ◽  
...  
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
The North

scholarly journals A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 720-732 ◽  
Author(s):  
Kasey K. Pham ◽  
Andrew L. Hipp ◽  
Paul S. Manos ◽  
Richard C. Cronn
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Introgressive Hybridization ◽  
White Oak ◽  
Gene Migration ◽  
The North ◽  
Geographic Structure ◽  
Phylogenetic Studies ◽  
Phylogenetic Informativeness ◽  
Lineage Divergence

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.

Combined phylogenetic analysis of ribosomal ITS1 sequences and new chromosome data supports three subgroups of Dolly Varden char (Salvelinus malma)

1999 ◽  
Vol 56 (8) ◽  
pp. 1504-1511 ◽  
Author(s):  
Ruth B Phillips ◽  
Linda I Gudex ◽  
Kathleen M Westrich ◽  
Alfred DeCicco
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Lake Trout ◽  
Salvelinus Alpinus ◽  
Dolly Varden ◽  
Salvelinus Malma ◽  
Dolly Varden Char ◽  
The North ◽  
Rdna Sequences ◽  
Kamchatka River

A phylogenetic analysis of the subspecies of Salvelinus malma (Dolly Varden char) was done using DNA sequences from the first internal transcribed spacer (ITS1) of the ribosomal DNA (rDNA). Sequences were obtained from the northern S. malma malma from the Noatak River, Alaska, and the Kamchatka River, Russia; from the southern North American form S. malma lordi from the Fox River, Kenai peninsula, and Auke Bay near Juneau, Alaska; and from the southern Asian form S. malma krascheninnikovi from Belaya River in Sakhalin Island, Russia. These sequences were combined with others from Salvelinus alpinus (Arctic char) from several locations in the North Pacific and Europe and analyzed using maximum parsimony and neighbor joining algorithms with Salvelinus namaycush (lake trout) as an outgroup. The resulting trees had two well-supported groups: S. m. malma and S. m. krascheninnikovi in one group and S. m. lordi and various populations of S. alpinus in the other. Salvelinus m. malma and S. m. krascheninnikovi were sister taxa, and S. m. lordi was most closely related to S. alpinus from Northwest Territories (S. a. erythrinus). New chromosome data from S. m. malma from northwestern Alaska supported the three named subspecies because S. m. malma from both Alaska and Russia have 2n = 78 compared with 2n = 82 for the two southern forms and the location of the nuclear organizer regions (NORs) was different in each of the three subspecies.

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