Inversions maintain differences between migratory phenotypes of a songbird

Long-distance migration requires adaptations in a suite of behavioral, physiological and morphological traits. However, almost nothing is known about the genetic basis of these adaptations. The willow warbler Phylloscopus trochilus occurs in Europe with a northern and southern subspecies that show drastically different migration routes and wintering areas. Previous studies have demonstrated that the subspecies are genetically extremely similar except for three divergent chromosome regions, of which two are associated with the differences in migratory phenotypes and one is associated with an environmental gradient. Here we use a combination of long-read sequencing, linked-read sequencing and optical mapping to construct more complete and contiguous assemblies for both of the subspecies. We find evidence for inversions in each of the three divergent regions, which range from 0.4 to 13 Mb in size, and that breakpoints are associated with tandem repeat arrays or segmental duplications. The divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where the inversions arose in either of two allopatric populations that subsequently hybridized. The improved genome assemblies and annotation also allowed us to detect additional functional differences in the divergent regions that provide candidate genes for migration and local adaptations to environmental gradients.

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Migratory connectivity and population-specific migration routes in a long-distance migratory bird

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.2897 ◽

2014 ◽

Vol 281 (1778) ◽

pp. 20132897 ◽

Cited By ~ 74

Author(s):

Christiane Trierweiler ◽

Raymond H. G. Klaassen ◽

Rudi H. Drent ◽

Klaus-Michael Exo ◽

Jan Komdeur ◽

...

Keyword(s):

Migratory Bird ◽

Habitat Characteristics ◽

Sub Saharan Africa ◽

Migratory Connectivity ◽

Migration Routes ◽

Long Distance ◽

Comprehensive Overview ◽

Migration System ◽

Breeding Populations ◽

Wintering Areas

Knowledge about migratory connectivity, the degree to which individuals from the same breeding site migrate to the same wintering site, is essential to understand processes affecting populations of migrants throughout the annual cycle. Here, we study the migration system of a long-distance migratory bird, the Montagu's harrier Circus pygargus , by tracking individuals from different breeding populations throughout northern Europe. We identified three main migration routes towards wintering areas in sub-Saharan Africa. Wintering areas and migration routes of different breeding populations overlapped, a pattern best described by ‘weak (diffuse) connectivity’. Migratory performance, i.e. timing, duration, distance and speed of migration, was surprisingly similar for the three routes despite differences in habitat characteristics. This study provides, to our knowledge, a first comprehensive overview of the migration system of a Palaearctic-African long-distance migrant. We emphasize the importance of spatial scale (e.g. distances between breeding populations) in defining patterns of connectivity and suggest that knowledge about fundamental aspects determining distribution patterns, such as the among-individual variation in mean migration directions, is required to ultimately understand migratory connectivity. Furthermore, we stress that for conservation purposes it is pivotal to consider wintering areas as well as migration routes and in particular stopover sites.

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

10.21203/rs.3.rs-712747/v1 ◽

2021 ◽

Author(s):

Arang Rhie ◽

Ann Mc Cartney ◽

Kishwar Shafin ◽

Michael Alonge ◽

Andrey Bzikadze ◽

...

Keyword(s):

Genome Assembly ◽

Tandem Repeats ◽

Hydatidiform Mole ◽

Segmental Duplications ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Human Genome Assembly ◽

Long Read ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

Abstract Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies

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mosaicFlye: Resolving long mosaic repeats using long error-prone reads

10.1101/2020.01.15.908285 ◽

2020 ◽

Cited By ~ 3

Author(s):

Anton Bankevich ◽

Pavel Pevzner

Keyword(s):

Human Chromosome ◽

Human Genome ◽

Genome Assembly ◽

Chromosome 6 ◽

Segmental Duplications ◽

Bacterial Genomes ◽

Long Read ◽

Human Chromosome 6 ◽

Genome Assemblies ◽

Eukaryotic Genomes

AbstractLong-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes. However, the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of bacterial genomes and metagenomes. We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of the human genome as well as bacterial genomes and metagenomes. In particular, we show that mosaicFlye results in a complete assembly of both arms of the human chromosome 6.

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Pair bonds during the annual cycle of a long-distance migrant, the Arctic Tern (Sterna paradisaea)

Avian Research ◽

10.1186/s40657-021-00268-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Chris P. F. Redfern

Keyword(s):

Annual Cycle ◽

Migratory Birds ◽

The Arctic ◽

Migration Routes ◽

Long Distance ◽

Breeding Colony ◽

Arrival Times ◽

Pair Bonds ◽

Sterna Paradisaea ◽

Wintering Areas

Abstract Background The extent to which pairs remain together during the annual cycle is a key question in the behavioural ecology of migratory birds. While a few species migrate and winter as family units, for most the extent to which breeding partners associate in the non-breeding season is unknown. The Arctic Tern (Sterna paradisaea) has one of the longest migrations of any species, and the aim of this study was to establish whether or not partners remain together after breeding. Methods Leg-mounted geolocators were fitted to breeding pairs of Arctic Terns nesting on the Farne Islands, Northumberland, UK. The devices were recovered for analysis the following year. Results Analysis of data for the six pairs which returned the following year showed that partners departed from the colony at different times after breeding and migrated independently to different Antarctic regions. Partners also departed from the Antarctic and turned to the breeding colony independently. One third of the pairs divorced on return. Conclusions For long-distance migrants reliant on unpredictable foraging opportunities, it may not be viable to remain as pairs away from the breeding colony. Synchrony in arrival times at the breeding colony may maximise the chance of retaining a familiar partner, but could be affected by environmental factors in wintering areas or along migration routes.

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Autumn migration routes and wintering areas of juvenile Chinese Egrets (Egretta eulophotes) revealed by GPS tracking

Avian Research ◽

10.1186/s40657-021-00297-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zhijun Huang ◽

Xiaoping Zhou ◽

Wenzhen Fang ◽

Hailong Zhang ◽

Xiaolin Chen

Keyword(s):

Coastal Wetlands ◽

The Philippines ◽

Autumn Migration ◽

Gps Tracking ◽

Migration Routes ◽

Long Distance ◽

The Pacific ◽

Wintering Areas ◽

Egretta Eulophotes ◽

Chinese Egret

Abstract Background The vulnerable Chinese Egret (Egretta eulophotes) is a long-distance migratory waterbird whose migration and wintering information is poorly understood. This study aims to identify the autumn migration routes and wintering areas of juvenile Chinese Egrets and determine the migration movement traits of this species. Methods Thirty-nine juvenile Chinese Egrets from the Fantuozi Island, an uninhabited offshore island with a large breeding colony of Chinese Egrets in Dalian, China, were tracked using GPS/GSM transmitters. Some feathers from each tracked juvenile were collected for molecular identification of sex in the laboratory. The GPS locations, recorded at 2-h intervals from August 2018 to May 2020, were used for the analyses. Results Of the 39 tracked juveniles, 30 individuals began their migration between September and November, and 13 successfully completed their autumn migration between October and November. The juveniles migrated southward via three migration routes, coastal, oceanic and inland, mainly during the night. The migration duration, migration distance, flight speed, and stopover duration of the 13 juvenile egrets that completed migration averaged 5.08 ± 1.04 days, 3928.18 ± 414.27 km, 57.27 ± 5.73 km/h, and 23.08 ± 19.28 h, respectively. These juveniles wintered in the coastal wetlands of Southeast Asia including those in the Philippines, Vietnam, and Malaysia, and only one successfully began its spring migration in June 2020. Conclusions This study newly finds that the oceanic route taken by juvenile Chinese Egrets, suggesting that the juveniles are able to fly over the Pacific Ocean without a stopover. Moreover, our novel data indicate that coastal wetlands along the East Asian–Australasian Flyway are important areas for both autumn migration stopover and the wintering of these juveniles, suggesting that international cooperation is important to conserve the vulnerable Chinese Egret and the wetland habitats on which it depends.

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

10.1101/2021.07.02.450803 ◽

2021 ◽

Author(s):

Ann M Mc Cartney ◽

Kishwar Shafin ◽

Michael Alonge ◽

Andrey V Bzikadze ◽

Giulio Formenti ◽

...

Keyword(s):

Genome Assembly ◽

Tandem Repeats ◽

Hydatidiform Mole ◽

Segmental Duplications ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Human Genome Assembly ◽

Long Read ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

Nature Communications ◽

10.1038/s41467-021-25435-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

PingHsun Hsieh ◽

Vy Dang ◽

Mitchell R. Vollger ◽

Yafei Mao ◽

Tzu-Hsueh Huang ◽

...

Keyword(s):

Copy Number ◽

Homo Sapiens ◽

Segmental Duplications ◽

Sensor Protein ◽

Long Read ◽

Number Variation ◽

Selective Forces ◽

Structural Mutations ◽

Cold Sensor ◽

Human Specific

AbstractTRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.

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Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab034 ◽

2021 ◽

Vol 3 (2) ◽

Author(s):

Jean-Marc Aury ◽

Benjamin Istace

Keyword(s):

Single Molecule ◽

Direct Consequence ◽

High Quality ◽

Sequencing Errors ◽

Coding Regions ◽

Sequencing Technologies ◽

Long Reads ◽

Oxford Nanopore ◽

Long Read ◽

Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

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Geomagnetic imprinting predicts spatio-temporal variation in homing migration of pink and sockeye salmon

Journal of The Royal Society Interface ◽

10.1098/rsif.2014.0542 ◽

2014 ◽

Vol 11 (99) ◽

pp. 20140542 ◽

Cited By ~ 41

Author(s):

Nathan F. Putman ◽

Erica S. Jenkins ◽

Catherine G. J. Michielsens ◽

David L. G. Noakes

Keyword(s):

Magnetic Field ◽

Temporal Variation ◽

Ocean Circulation ◽

Sockeye Salmon ◽

Movement Patterns ◽

Oncorhynchus Gorbuscha ◽

Migration Routes ◽

Long Distance ◽

Spatio Temporal ◽

Olfactory Imprinting

Animals navigate using a variety of sensory cues, but how each is weighted during different phases of movement (e.g. dispersal, foraging, homing) is controversial. Here, we examine the geomagnetic and olfactory imprinting hypotheses of natal homing with datasets that recorded variation in the migratory routes of sockeye ( Oncorhynchus nerka ) and pink ( Oncorhynchus gorbuscha ) salmon returning from the Pacific Ocean to the Fraser River, British Columbia. Drift of the magnetic field (i.e. geomagnetic imprinting) uniquely accounted for 23.2% and 44.0% of the variation in migration routes for sockeye and pink salmon, respectively. Ocean circulation (i.e. olfactory imprinting) predicted 6.1% and 0.1% of the variation in sockeye and pink migration routes, respectively. Sea surface temperature (a variable influencing salmon distribution but not navigation, directly) accounted for 13.0% of the variation in sockeye migration but was unrelated to pink migration. These findings suggest that geomagnetic navigation plays an important role in long-distance homing in salmon and that consideration of navigation mechanisms can aid in the management of migratory fishes by better predicting movement patterns. Finally, given the diversity of animals that use the Earth's magnetic field for navigation, geomagnetic drift may provide a unifying explanation for spatio-temporal variation in the movement patterns of many species.

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