scholarly journals Range Overlap Drives Chromosome Inversion Fixation in Passerine Birds

2016 ◽  
Author(s):  
Daniel M. Hooper
Keyword(s):  
Pericentric Inversion ◽  
Sex Chromosome ◽  
Gc Content ◽  
Divergence Times ◽  
Passerine Birds ◽  
Genomic Context ◽  
Chromosome Inversion ◽  
Closely Related Species ◽  
Chromosome Inversions ◽  
Range Overlap

Chromosome inversions evolve frequently but the reasons why remain largely enigmatic. I used cytological descriptions of 410 species of passerine birds (order Passeriformes) to identify pericentric inversion differences between species. Using a new fossil-calibrated phylogeny I examine the phylogenetic, demographic, and genomic context in which these inversions have evolved. The number of inversion differences between closely related species was highly variable yet consistently predicted by a single factor: whether the ranges of species overlapped. This observation holds even when the analysis is restricted to sympatric sister pairs known to hybridize, and which have divergence times estimated similar to allopatric pairs. Inversions were significantly more likely to have fixed on a sex chromosome than an autosome yet variable mutagenic input alone (by chromosome size, map length, GC content, or repeat density) cannot explain the differences between chromosomes in the number of inversions fixed. Together, these results support a model in which inversions in passerines are adaptive and spread by selection when gene flow occurs before reproductive isolation is complete.

Differential occurrence of chromosome inversion polymorphisms among Muller's elements in three species of the tripunctata group of Drosophila, including a species with fast chromosomal evolution

Genome ◽  
2013 ◽  
Vol 56 (1) ◽  
pp. 17-26 ◽  
Author(s):  
Mitsue T. Brianti ◽  
Galina Ananina ◽  
Louis B. Klaczko
Keyword(s):  
Pericentric Inversion ◽  
Chromosome Pair ◽  
Genetic Architecture ◽  
Polytene Chromosomes ◽  
Chromosomal Evolution ◽  
Chromosome Inversion ◽  
Closely Related Species ◽  
Chromosome Inversions ◽  
Chromosome Maps ◽  
Chromosome Fusions

Detailed chromosome maps with reliable homologies among chromosomes of different species are the first step to study the evolution of the genetic architecture in any set of species. Here, we present detailed photo maps of the polytene chromosomes of three closely related species of the tripunctata group (subgenus Drosophila): Drosophila mediopunctata, D. roehrae, and D. unipunctata. We identified Muller's elements in each species, using FISH, establishing reliable chromosome homologies among species and D. melanogaster. The simultaneous analysis of chromosome inversions revealed a distribution pattern for the inversion polymorphisms among Muller's elements in the three species. Element E is the most polymorphic, with many inversions in each species. Element C follows; while the least polymorphic elements are B and D. While interesting, it remains to be determined how general this pattern is among species of the tripunctata group. Despite previous studies showing that D. mediopunctata and D. unipunctata are phylogenetically closer to each other than to D. roehrae, D. unipunctata shows rare karyotypic changes. It has two chromosome fusions: an additional heterochromatic chromosome pair and a pericentric inversion in the X chromosome. This especial conformation suggests a fast chromosomal evolution that deserves further study.

scholarly journals Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

2020 ◽  
Vol 10 (5) ◽  
pp. 1553-1561 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Network Analysis ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

scholarly journals Patterns of linkage disequilibrium reveal genome architecture in chum salmon

2019 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Linkage Disequilibrium ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions ◽  
Sexually Antagonistic Selection ◽  
Gene Complexes

AbstractMany studies exclude loci exhibiting linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the signal of the sex-determining region was only obvious after restricting genetic analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. The results of this study highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of ignoring or excluding loci exhibiting LD.

scholarly journals Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration

2020 ◽  
Vol 12 (4) ◽  
pp. 243-258 ◽  
Author(s):  
Wen-Juan Ma ◽  
Fantin Carpentier ◽  
Tatiana Giraud ◽  
Michael E Hood
Keyword(s):  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Mating Type ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Gc Content ◽  
Differentially Expressed ◽  
Mating Types ◽  
Sexual Antagonism ◽  
Recombination Suppression

Abstract Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.

scholarly journals A sex chromosome inversion is associated with copy number variation of mitochondrial DNA in zebra finch sperm

2019 ◽  
Author(s):  
Ulrich Knief ◽  
Wolfgang Forstmeier ◽  
Bart Kempenaers ◽  
Jochen B. W. Wolf
Keyword(s):  
Mitochondrial Dna ◽  
Zebra Finch ◽  
Copy Number ◽  
Sex Chromosome ◽  
Data Availability ◽  
Species Variation ◽  
Zebra Finches ◽  
Chromosome Inversion ◽  
Atp Production ◽  
Sperm Midpiece

AbstractPropulsion of sperm cells via movement of the flagellum is of vital importance for successful fertilization. Presumably, the energy for this movement comes from the mitochondria in the sperm midpiece. Larger midpieces may contain more mitochondria, which should enhance the energetic capacity and hence promote mobility. Due to an inversion polymorphism on their sex chromosome TguZ, zebra finches (Taeniopygia guttata castanotis) exhibit large within-species variation in sperm midpiece length, and those sperm with the longest midpieces swim the fastest. Here, we test through quantitative real-time PCR in zebra finch ejaculates whether the inversion genotype has an effect on the copy number of mitochondrial DNA. Taking the inversion genotype as a proxy for midpiece length, we find that zebra finches with longer midpieces indeed have more copies of the mitochondrial DNA in their ejaculates than those with shorter midpieces, with potential downstream effects on the rate of ATP production and sperm swimming speed. This study sheds light on the proximate cause of a fitness-relevant genetic polymorphism, suggesting the involvement of central components of gamete energy metabolism.Data availabilitySupplementary data file

scholarly journals Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

2021 ◽  
Author(s):  
Else K. Mikkelsen ◽  
Darren Irwin
Keyword(s):  
First Generation ◽  
Sex Chromosome ◽  
Genomic Variation ◽  
F1 Hybrids ◽  
The Pacific ◽  
Species Pairs ◽  
Genetic Clusters ◽  
Range Overlap ◽  
Female Specific

AbstractContact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren (Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.

scholarly journals Chromosomal Evolution in the Lizard Genus Varanus (Reptilia)

1975 ◽  
Vol 28 (1) ◽  
pp. 89 ◽  
Author(s):  
Max Kinga ◽  
Dennis King
Keyword(s):  
Chromosome Number ◽  
Pericentric Inversion ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Size Groups ◽  
Sex Chromosome System

The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 pairs of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromere shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZjZW type was present in a number of the species examined.

scholarly journals Draft Genome of the Macadamia Husk Spot Pathogen, Pseudocercospora macadamiae

2020 ◽  
Vol 110 (9) ◽  
pp. 1503-1506
Author(s):  
Olufemi A. Akinsanmi ◽  
Lilia C. Carvalhais
Keyword(s):  
Plant Disease Resistance ◽  
Plant Disease ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Disease Development ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family

Pseudocercospora macadamiae causes husk spot in macadamia in Australia. Lack of genomic resources for this pathogen has restricted acquiring knowledge on the mechanism of disease development, spread, and its role in fruit abscission. To address this gap, we sequenced the genome of P. macadamiae. The sequence was de novo assembled into a draft genome of 40 Mb, which is comparable to closely related species in the family Mycosphaerellaceae. The draft genome comprises 212 scaffolds, of which 99 scaffolds are over 50 kb. The genome has a 49% GC content and is predicted to contain 15,430 protein-coding genes. This draft genome sequence is the first for P. macadamiae and represents a valuable resource for understanding genome evolution and plant disease resistance.

scholarly journals Chromosome and Genome Divergence between the Cryptic Eurasian Malaria Vector-Species Anopheles messeae and Anopheles daciae

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 165 ◽  
Author(s):  
Anastasia N. Naumenko ◽  
Dmitriy A. Karagodin ◽  
Andrey A. Yurchenko ◽  
Anton V. Moskaev ◽  
Olga I. Martin ◽  
...  
Keyword(s):  
X Chromosome ◽  
Malaria Vector ◽  
Its2 Region ◽  
Nucleotide Substitutions ◽  
Closely Related Species ◽  
Chromosomal Inversions ◽  
Chromosome Inversions ◽  
Genome Wide ◽  
Genome Divergence ◽  
Incomplete Reproductive Isolation

Chromosomal inversions are important drivers of genome evolution. The Eurasian malaria vector Anopheles messeae has five polymorphic inversions. A cryptic species, An. daciae, has been discriminated from An. messeae based on five fixed nucleotide substitutions in the internal transcribed spacer 2 (ITS2) of ribosomal DNA. However, the inversion polymorphism in An. daciae and the genome divergence between these species remain unexplored. In this study, we sequenced the ITS2 region and analyzed the inversion frequencies of 289 Anopheles larvae specimens collected from three locations in the Moscow region. Five individual genomes for each of the two species were sequenced. We determined that An. messeae and An. daciae differ from each other by the frequency of polymorphic inversions. Inversion X1 was fixed in An. messeae but polymorphic in An. daciae populations. The genome sequence comparison demonstrated genome-wide divergence between the species, especially pronounced on the inversion-rich X chromosome (mean Fst = 0.331). The frequency of polymorphic autosomal inversions was higher in An. messeae than in An. daciae. We conclude that the X chromosome inversions play an important role in the genomic differentiation between the species. Our study determined that An. messeae and An. daciae are closely related species with incomplete reproductive isolation.

FILIAL SOCIAL BOND FORMATION IN FRY OF THE MATERNAL MOUTHBROODING TILAPIA (PISCES: CICHLIDAE): A COMPARATIVE STUDY

Behaviour ◽  
1999 ◽  
Vol 136 (5) ◽  
pp. 567-594 ◽  
Author(s):  
Howard Russock
Keyword(s):  
Response Pattern ◽  
Bond Formation ◽  
Cichlid Fish ◽  
Significant Decline ◽  
Song Learning ◽  
Social Bond ◽  
Sensitive Period ◽  
Passerine Birds ◽  
Closely Related Species ◽  
Precocial Birds

AbstractThe mother - fry relationship in the maternal mouthbrooding species of tilapia has become a model of social bond formation in fish because of the relatively extensive care given to the young. This relationship has been extensively studied in Oreochromis mossambicus. In order to determine if the response pattern observed in O. mossambicus fry has broader applications, the critical experiments of these studies were replicated in two closely related species of maternal mouthbrooding tilapia, O. niloticus and O. esculentus. All fry used in the study were removed from their mother's mouth as eggs and hatched artificially in groups. The fry were also exposed to maternal models in groups, but all fry in the study were tested for their responsiveness or preferential behaviour to maternal models individually. Experiment I determined the responsiveness of fry naive to maternal models in order to establish a baseline for future comparisons. O. niloticus fry exhibited a significant decline in responsiveness to models between days 11 and 12 post-hatching while O. esculentus fry exhibited a significant decline between days 16 and 18, suggesting the possible existence of a sensitive period in these two species. In order to obtain evidence for the existence of a sensitive period, naive fry of both species in Experiment II were exposed to maternal models at their peak of responsiveness and then tested at a later age at which responsiveness in naive fry had fallen significantly. In 15 of the 18 comparisons involving the two species, exposure to a maternal model at the peak of responsiveness for naive fry prevented the later decline in responsiveness. Experiment III examined whether experience with maternal models effected how exclusively fry responded to such models in the future. It was predicted that, like O. mossambicus fry, experienced fry of both species would exhibit a decline in responsiveness to models that formed at least a partial mismatch with the fry's initial schema for maternal stimuli. This prediction was not supported. Experiment IV examined preferential behaviour. It was predicted that fry exposed to a maternal model would later behave preferentially toward whichever model of a pair formed a closer match with their schema, and not necessarily toward the model to which they had been previously exposed. Maternally naive fry were not expected to behave preferentially. These predictions were generally supported, although the effect was less vigorous or consistent than in O. mossambicus. Filial social bond formation in these species of maternal mouthbrooding tilapia appears to be characterized by strong predispositions for maternally relevant visual stimuli which require appropriate experience for their maintenance and for the induction of preferences. Since a similar developmental pattern in seen in (e.g.) song learning in passerine birds, imprinting in precocial birds and filial following in substrate spawning cichlid fish, the phenomenon appears to be of broad significance.

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