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Journal articles on the topic 'Ancestral genomes'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

Schaefer, Nathan K., Beth Shapiro, and Richard E. Green. "An ancestral recombination graph of human, Neanderthal, and Denisovan genomes." Science Advances 7, no. 29 (2021): eabc0776. http://dx.doi.org/10.1126/sciadv.abc0776.

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Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map w

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RASCOL, V., P. PONTAROTTI, and A. LEVASSEUR. "Ancestral animal genomes reconstruction." Current Opinion in Immunology 19, no. 5 (2007): 542–46. http://dx.doi.org/10.1016/j.coi.2007.06.009.

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Lee, Daehwan, Jongin Lee, Woon-Young Hong, Eunji Jang, and Jaebum Kim. "AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes." Journal of KIISE 42, no. 12 (2015): 1584–89. http://dx.doi.org/10.5626/jok.2015.42.12.1584.

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4

Xu, Qiaoji, Lingling Jin, James H. Leebens-Mack, and David Sankoff. "Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order." Algorithms 14, no. 6 (2021): 160. http://dx.doi.org/10.3390/a14060160.

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The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process givin

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Avdeyev, Pavel, Nikita Alexeev, Yongwu Rong, and Max A. Alekseyev. "A unified ILP framework for core ancestral genome reconstruction problems." Bioinformatics 36, no. 10 (2020): 2993–3003. http://dx.doi.org/10.1093/bioinformatics/btaa100.

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Abstract Motivation One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole-genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of preduplicated

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Ouzounis, Christos A. "Ancestral state reconstructions for genomes." Current Opinion in Genetics & Development 15, no. 6 (2005): 595–600. http://dx.doi.org/10.1016/j.gde.2005.09.011.

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7

Jones, B. R., A. Rajaraman, E. Tannier, and C. Chauve. "ANGES: reconstructing ANcestral GEnomeS maps." Bioinformatics 28, no. 18 (2012): 2388–90. http://dx.doi.org/10.1093/bioinformatics/bts457.

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Pompidor, Nicolas, Carine Charron, Catherine Hervouet, et al. "Three founding ancestral genomes involved in the origin of sugarcane." Annals of Botany 127, no. 6 (2021): 827–40. http://dx.doi.org/10.1093/aob/mcab008.

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Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among repre

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Huang, Xiaosong, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, and Paul D. Thomas. "Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life." Nucleic Acids Research 47, no. D1 (2018): D271—D279. http://dx.doi.org/10.1093/nar/gky1009.

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10

Guyot, Romain, and Beat Keller. "Ancestral genome duplication in rice." Genome 47, no. 3 (2004): 610–14. http://dx.doi.org/10.1139/g04-016.

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The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >

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Waters, Elizabeth R., and Barbara A. Schaal. "Biased gene conversion is not occurring among rDNA repeats in the Brassica triangle." Genome 39, no. 1 (1996): 150–54. http://dx.doi.org/10.1139/g96-020.

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Hybridization is a common phenomenon that results in complex genomes. How ancestral genomes interact in hybrids has long been of great interest. Recombination among ancestral genomes may increase or decrease genetic variation. This study examines rDNA from members of the Brassica triangle for evidence of gene conversion across ancestral genomes. Gene conversion is a powerful force in the evolution of multigene families. It has previously been shown that biased gene conversion can act to homogenize rDNA repeats within hybrid genomes. Here, we find no evidence for biased gene conversion or unequ

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Pena, Sérgio DJ, Carlos Renato Machado, and Andréa Mara Macedo. "Trypanosoma cruzi: ancestral genomes and population structure." Memórias do Instituto Oswaldo Cruz 104, suppl 1 (2009): 108–14. http://dx.doi.org/10.1590/s0074-02762009000900016.

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13

Nguyen, Thao Thi Phuong, Vinh Sy Le, Hai Bich Ho, and Quang Si Le. "Building Ancestral Recombination Graphs for Whole Genomes." IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, no. 2 (2017): 478–83. http://dx.doi.org/10.1109/tcbb.2016.2542801.

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Satou, Yutaka, Shuichi Wada, Yasunori Sasakura, and Nori Satoh. "Regulatory genes in the ancestral chordate genomes." Development Genes and Evolution 218, no. 11-12 (2008): 715–21. http://dx.doi.org/10.1007/s00427-008-0219-y.

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15

Durstewitz, G., A. Polley, J. Plieske, et al. "SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”." Genome 53, no. 11 (2010): 948–56. http://dx.doi.org/10.1139/g10-079.

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Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape

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Belyayev, Alexander, Olga Raskina, Abraham Korol, and Eviatar Nevo. "Coevolution of A and B genomes in allotetraploid Triticum dicoccoides." Genome 43, no. 6 (2000): 1021–26. http://dx.doi.org/10.1139/g00-060.

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Data is presented on the coevolution of A and B genomes in allotetraploid wheat Triticum dicoccoides (2n = 4x = 28, genome AABB) obtained by genomic in situ hybridization (GISH). Probing chromosomes of T. dicoccoides with DNA from the proposed A/B diploid genome ancestors shows evidence of enriching A-genome with repetitive sequences of B-genome type. Thus, ancestral S-genome sequences have spread throughout the AB polyploid genome to a greater extent than have ancestral A-genome sequences. The substitution of part of the A-genome heterochromatin clusters by satellite DNA of the B genome is de

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Hasegawa, Masami, Bojian Zhong, and Yang Zhong. "Adaptive evolution of chloroplast genomes in ancestral grasses." Plant Signaling & Behavior 4, no. 7 (2009): 623–24. http://dx.doi.org/10.4161/psb.4.7.8914.

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18

Logacheva, Maria D., Mikhail I. Schelkunov, Aleksey N. Fesenko, Artem S. Kasianov, and Aleksey A. Penin. "Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat." Plants 9, no. 5 (2020): 618. http://dx.doi.org/10.3390/plants9050618.

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Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long r

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Kurland, C. G., and S. G. E. Andersson. "Origin and Evolution of the Mitochondrial Proteome." Microbiology and Molecular Biology Reviews 64, no. 4 (2000): 786–820. http://dx.doi.org/10.1128/mmbr.64.4.786-820.2000.

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SUMMARY The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral α-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from α-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-m

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Tusso, Sergio, Bart P. S. Nieuwenhuis, Fritz J. Sedlazeck, John W. Davey, Daniel C. Jeffares, and Jochen B. W. Wolf. "Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast." Molecular Biology and Evolution 36, no. 9 (2019): 1975–89. http://dx.doi.org/10.1093/molbev/msz126.

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Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alt

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Zhang, Hong-Bin, and Jan Dvořák. "The genome origin and evolution of hexaploid Triticum crassum and Triticum syriacum determined from variation in repeated nucleotide sequences." Genome 35, no. 5 (1992): 806–14. http://dx.doi.org/10.1139/g92-123.

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Hexaploid Triticum crassum Aitch &Hemsl. (syn. Aegilops crassa Boiss.) and Triticum syriacum Bowden [syn. Aegilops crassa Boiss. var. palaestina Eig, Aegilops vavilovii (Zhuk.) Chen.] are members of the T. crassum complex. Previous studies suggested that they have the D genomes of T. tauschii (Coss.) Schmalh., but the sources of the other genomes of these species remain uncertain. In the present investigation, variation in 27 repeated nucleotide sequences and the 5S rRNA loci was used to determine the genome origin of these hexaploid species. This study indicated that the two hexaploid spe

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Julca, Irene, Marina Marcet-Houben, Fernando Cruz, et al. "Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha." Molecular Biology and Evolution 37, no. 3 (2019): 730–56. http://dx.doi.org/10.1093/molbev/msz261.

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Abstract Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the availabl

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Speidel, Leo, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, and Simon R. Myers. "Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies." Molecular Biology and Evolution 38, no. 9 (2021): 3497–511. http://dx.doi.org/10.1093/molbev/msab174.

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Abstract Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coa

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Nelson, Matthew N., Isobel A. P. Parkin, and Derek J. Lydiate. "The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome." Genome 54, no. 1 (2011): 33–41. http://dx.doi.org/10.1139/g10-097.

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The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassi

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Ponting, Chris P., and Leo Goodstadt. "Separating derived from ancestral features of mouse and human genomes." Biochemical Society Transactions 37, no. 4 (2009): 734–39. http://dx.doi.org/10.1042/bst0370734.

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To take full advantage of the mouse as a model organism, it is essential to distinguish lineage-specific biology from what is shared between human and mouse. Investigations into shared genetic elements common to both have been well served by the draft human and mouse genome sequences. More recently, the virtually complete euchromatic sequences of the two reference genomes have been finished. These reveal a high (∼5%) level of sequence duplications that had previously been recalcitrant to sequencing and assembly. Within these duplications lie large numbers of rodent- or primate-specific genes.

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Clark, Alvin J., Mauricio Pontes, Tait Jones, and Colin Dale. "A Possible Heterodimeric Prophage-Like Element in the Genome of the Insect Endosymbiont Sodalis glossinidius." Journal of Bacteriology 189, no. 7 (2007): 2949–51. http://dx.doi.org/10.1128/jb.00913-06.

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ABSTRACT Extrachromosomal element pSOG3 (52,162 nucleotides) in the genome of Sodalis glossinidius contains redundant phage-related gene pairs, indicating that it may have been formed by the fusion of two ancestral phage genomes followed by gene degradation. We suggest that pSOG3 is a prophage that has undergone genome degeneration accompanying host adaptation to symbiosis.

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Wei, Shu-jun, Min Shi, Jun-hua He, M. Sharkey, and Xue-xin Chen. "The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events." Genome 52, no. 4 (2009): 308–19. http://dx.doi.org/10.1139/g09-008.

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Few complete mitochondrial genomes representing limited families in the order Hymenoptera have been sequenced. Here, we sequenced the complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae). This genome is 18 728 bp long, the second largest hexapod mitochondrial genome sequenced in its entirety and that with the highest A+T content at 87.4%. Four tRNAs are rearranged compared with the ancestral arrangement. Gene rearrangement mechanisms are different among all three rearranged regions. Six tRNAs have a large variable loop, which is not found in other metazoan mitocho

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Marcussen, T., S. R. Sandve, L. Heier, et al. "Ancient hybridizations among the ancestral genomes of bread wheat." Science 345, no. 6194 (2014): 1250092. http://dx.doi.org/10.1126/science.1250092.

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Johnson, Nicholas A., Marc A. Coram, Mark D. Shriver, et al. "Ancestral Components of Admixed Genomes in a Mexican Cohort." PLoS Genetics 7, no. 12 (2011): e1002410. http://dx.doi.org/10.1371/journal.pgen.1002410.

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Łukasik, Piotr, Katherine Nazario, James T. Van Leuven, et al. "Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas." Proceedings of the National Academy of Sciences 115, no. 2 (2017): E226—E235. http://dx.doi.org/10.1073/pnas.1712321115.

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Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades. To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six

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Cameron, Stephen L., Mark Dowton, Lyda R. Castro, et al. "Mitochondrial genome organization and phylogeny of two vespid wasps." Genome 51, no. 10 (2008): 800–808. http://dx.doi.org/10.1139/g08-066.

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We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the V

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Deakin, Janine E., and Rachel J. O'Neill. "Evolution of Marsupial Genomes." Annual Review of Animal Biosciences 8, no. 1 (2020): 25–45. http://dx.doi.org/10.1146/annurev-animal-021419-083555.

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Marsupial genomes, which are packaged into large chromosomes, provide a powerful resource for studying the mechanisms of genome evolution. The extensive and valuable body of work on marsupial cytogenetics, combined more recently with genome sequence data, has enabled prediction of the 2 n = 14 karyotype ancestral to all marsupial families. The application of both chromosome biology and genome sequencing, or chromosomics, has been a necessary approach for various aspects of mammalian genome evolution, such as understanding sex chromosome evolution and the origin and evolution of transmissible t

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Dvořák, Jan, Pantaleo di Terlizzi, Hong-Bin Zhang, and Paolo Resta. "The evolution of polyploid wheats: identification of the A genome donor species." Genome 36, no. 1 (1993): 21–31. http://dx.doi.org/10.1139/g93-004.

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Cytogenetic work has shown that the tetraploid wheats, Triticum turgidum and T. timopheevii, and the hexaploid wheat T. aestivum have one pair of A genomes, whereas hexaploid T. zhukovskyi has two. Variation in 16 repeated nucleotide sequences was used to identify sources of the A genomes. The A genomes of T. turgidum, T. timopheevii, and T. aestivum were shown to be contributed by T. urartu. Little divergence in the repeated nucleotide sequences was detected in the A genomes of these species from the genome of T. urartu. In T. zhukovskyi one A genome was contributed by T. urartu and the other

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Eisfeldt, Jesper, Gustaf Mårtensson, Adam Ameur, Daniel Nilsson, and Anna Lindstrand. "Discovery of Novel Sequences in 1,000 Swedish Genomes." Molecular Biology and Evolution 37, no. 1 (2019): 18–30. http://dx.doi.org/10.1093/molbev/msz176.

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Abstract Novel sequences (NSs), not present in the human reference genome, are abundant and remain largely unexplored. Here, we utilize de novo assembly to study NS in 1,000 Swedish individuals first sequenced as part of the SweGen project revealing a total of 46 Mb in 61,044 distinct contigs of sequences not present in GRCh38. The contigs were aligned to recently published catalogs of Icelandic and Pan-African NSs, as well as the chimpanzee genome, revealing a great diversity of shared sequences. Analyzing the positioning of NS across the chimpanzee genome, we find that 2,807 NS align confide

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Finke, Kelly, Michael Kourakos, Gabriela Brown, et al. "Ancestral haplotype reconstruction in endogamous populations using identity-by-descent." PLOS Computational Biology 17, no. 2 (2021): e1008638. http://dx.doi.org/10.1371/journal.pcbi.1008638.

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In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of o

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ZHOU, ZHONG, MELVIN ZHANG, FANCHANG HAO, and HON WAI LEONG. "ON TWO VARIATIONS OF THE REVERSAL MEDIAN PROBLEM." International Journal of Modern Physics: Conference Series 09 (January 2012): 285–92. http://dx.doi.org/10.1142/s2010194512005338.

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We have developed an exact algorithm that solves certain instances of the Reversal Median Problem (RMP) when provided with additional input – the optimal sorting sequences between every pair of genomes. Our algorithm is able to provide an exact solution (the median genome) or determine that it is not able to do so for every instance of the problem. We have also proven the correctness of the algorithm in a theorem. RMP is the problem of finding an ancestral genome (the median) given the gene orders of three genomes. It is commonly encountered when constructing phylogeny, and is NP-hard. Two var

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Civáň, Peter, Peter G. Foster, Martin T. Embley, Ana Séneca, and Cymon J. Cox. "Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants." Genome Biology and Evolution 6, no. 4 (2014): 897–911. http://dx.doi.org/10.1093/gbe/evu061.

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Forster, Peter, Lucy Forster, Colin Renfrew, and Michael Forster. "Phylogenetic network analysis of SARS-CoV-2 genomes." Proceedings of the National Academy of Sciences 117, no. 17 (2020): 9241–43. http://dx.doi.org/10.1073/pnas.2004999117.

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In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing

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Eberle, Karolin E., Samy Sayed, Mohammedreza Rezapanah, Sharareh Shojai-Estabragh, and Johannes A. Jehle. "Diversity and evolution of the Cydia pomonella granulovirus." Journal of General Virology 90, no. 3 (2009): 662–71. http://dx.doi.org/10.1099/vir.0.006999-0.

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Eight new field isolates of Cydia pomonella granulovirus (CpGV) originating in Iran and Georgia and one English CpGV isolate were analysed for restriction fragment length polymorphisms (RFLPs) and by partial genome amplification and sequencing. According to the observed RFLPs, most of the predominant genotypes of these isolates could be assigned to those present in previously found isolates originating from Mexico (CpGV-M), England (CpGV-E) and Russia (CpGV-R). We suggest that these isolates should be designated genome A, B and C types, respectively. A fourth genome type was identified in thre

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Wächtershäuser, Günter. "Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment." Systematic and Applied Microbiology 21, no. 4 (1998): 473–77. http://dx.doi.org/10.1016/s0723-2020(98)80058-1.

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Rocchi, M., N. Archidiacono, and R. Stanyon. "Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed." Genome Research 16, no. 12 (2006): 1441–44. http://dx.doi.org/10.1101/gr.5687906.

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Green, R. E., E. L. Braun, J. Armstrong, et al. "Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs." Science 346, no. 6215 (2014): 1254449. http://dx.doi.org/10.1126/science.1254449.

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Zhong, Bojian, Takahiro Yonezawa, Yang Zhong, and Masami Hasegawa. "Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses." PLoS ONE 4, no. 4 (2009): e5297. http://dx.doi.org/10.1371/journal.pone.0005297.

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de Freitas, Jorge M., Luiz Augusto-Pinto, Juliana R. Pimenta, et al. "Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi." PLoS Pathogens 2, no. 3 (2006): e24. http://dx.doi.org/10.1371/journal.ppat.0020024.

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Deng, Jiabin, Gang Gao, Yan Zhang, et al. "Phylogenetic and ancestral area reconstruction of Zingiberales from plastid genomes." Biochemical Systematics and Ecology 66 (June 2016): 123–28. http://dx.doi.org/10.1016/j.bse.2016.03.013.

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Cottin, Aurélien, Benjamin Penaud, Jean-Christophe Glaszmann, Nabila Yahiaoui, and Mathieu Gautier. "Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes." G3: Genes|Genomes|Genetics 10, no. 2 (2019): 569–79. http://dx.doi.org/10.1534/g3.119.400873.

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Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios tha

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Fahrein, Kathrin, Susan E. Masta, and Lars Podsiadlowski. "The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order." Genome 52, no. 5 (2009): 456–66. http://dx.doi.org/10.1139/g09-023.

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Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning

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Chak, Solomon T. C., Stephen E. Harris, Kristin M. Hultgren, Nicholas W. Jeffery, and Dustin R. Rubenstein. "Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements." Proceedings of the National Academy of Sciences 118, no. 24 (2021): e2025051118. http://dx.doi.org/10.1073/pnas.2025051118.

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Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repet

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Wright, Joanne L., Sally Wasef, Tim H. Heupink, et al. "Ancient nuclear genomes enable repatriation of Indigenous human remains." Science Advances 4, no. 12 (2018): eaau5064. http://dx.doi.org/10.1126/sciadv.aau5064.

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After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the prese

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Nakatani, Yoichiro, and Aoife McLysaght. "Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes." Bioinformatics 33, no. 14 (2017): i369—i378. http://dx.doi.org/10.1093/bioinformatics/btx259.

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