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Background In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe ( Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian ( G. camelopardalis camelopardalis ), reticulated ( G. reticulata ), and Masai giraffe sensu stricto ( G. tippelskirchi tippelskirchi ) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. Results We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. Conclusions Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.

A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees with fossil-calibrated dates. The ancestral Bombus lineage was estimated to diversify between 47.08 and 34.27 million years ago (Ma) in the Holarctic region, but largely restricted to the eastern Old World. The Neotropical region was initially colonized in the Late Miocene, where bumblebee diversification was shown to be consistent with geologic and climatic events of the Late Cenozoic. Neotropical bumblebees likely originated from Nearctic lineages, which dispersed towards South America after 29 Ma.

Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.

The giant anteater (Myrmecophaga tridactyla) is a strictly myrmecophagous xenarthran species that ranges from Honduras to northern Argentina, occupying various habitats, from grassland and floodplains to forests. According to the IUCN, it is a vulnerable species mainly threatened by poaching, habitat loss and fragmentation, and road kills. Here, we investigate the phylogeography, distribution, ecology, and historical demography of Brazilian populations of the giant anteater. We analysed two mitochondrial (mtDNA) and three nuclear (nDNA) markers in 106 individuals from the Cerrado, Pantanal, Atlantic Forest, and Amazon Forest biomes through analyses of population structure and demography, phylogeography, and ecological niche modelling. Two divergent mtDNA clusters were found, one in the Amazon (AM) and another in the Cerrado, Pantanal, and Atlantic Forest biomes (CEPTAF). At the population level, CEPTAF presented higher mtDNA haplotype richness than AM and a unidirectional mtDNA gene flow was identified from AM to CEPTAF, which could be linked to more favourable habitat conditions for the species in Cerrado and Pantanal. Paleodemographic reconstructions with mtDNA and nDNA data indicate a large population expansion of the species starting at the end of the Pleistocene. Finally, the integrative phylogeographic analyses of giant anteater populations reinforce the importance of the Brazilian Cerrado as a priority biome for the species’ conservation.

Historically, giraffe have been translocated across Africa to supplement extant populations, reintroduce extinct populations or to establish new populations, often for conservation and tourism. Such faunal relocations were often carried out disregarding taxonomic affiliation. Today, the small giraffe populations in the Republic of Malawi are assumed to consist of South African giraffe (Giraffa giraffa giraffa), which have likely descended from five individuals translocated from Imire Game Park (Zimbabwe) to Nyala Game Park (Malawi) in 1993. However, during the last 25 years, unknown additional translocations, migrations or unrecognized local populations of potential Masai giraffe (Giraffa tippelskirchi) in Malawi may have resulted in introgressive hybridization. Thus, the current taxonomic affiliation for Malawi’s giraffe is uncertain, calling for a genetic assessment to implement further management. We analyzed mitochondrial sequences and nuclear introns for 14 individuals, representing approximately half of the known Malawian population, to genetically determine the (sub)species of giraffe that occur in the Republic of Malawi by comparison with a comprehensive Giraffa dataset. Additionally, we genotyped individuals at ten microsatellite loci to determine the level of inbreeding and potential introgression. All data identify individuals unambiguously as South African giraffe, although two individuals shared a single nuclear allele with Masai giraffe. The low microsatellite genetic variability suggests high inbreeding in the current population. Thus, supplementing Malawi’s giraffe populations with G. g. giraffa will prevent further loss of their genetic diversity and avoid inbreeding depression.

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

Background The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.

Abstract Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiforms such as seahorses and pipefishes. Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp, a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% of complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.66%. Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses. Competing Interest Statement The authors have declared no competing interest. Footnotes * e-mail, Sven Winter sven.winter{at}senckenberg.de, Stefan Prost stefanprost.research{at}protonmail.com, Jordi de Raad jordi.de_raad{at}senckenberg.de, Raphael T.F. Coimbra raphael.coimbra{at}senckenberg.de, Magnus Wolf magnus.wolf{at}senckenberg.de, Marcel Nebenführ marcel.nebenfuehr{at}senckenberg.de, Annika Held held-annika{at}gmx.de, Melina Kurzawe melina.kurzawe{at}gmx.de, Ramona Papapostolou ramona.papapostolou{at}stud.uni-frankfurt.de, Jade Tessien jade.tessien{at}hotmail.com, Julian Bludau julian.bludau{at}gmx.de, Andreas Kelch andreaskelch{at}gmx.de, Sarah Gronefeld sarah10gronefeld{at}gmail.com, Yannis Schöneberg yannis.schoeneberg{at}gmx.de, Christian Zeitz Christian.Zeitz{at}stud.uni-frankfurt.de, Konstantin Zapf konstantin{at}zapf-wetter.de, David Prochotta davidprochotta{at}hotmail.com, Maximilian Murphy ulthwe1{at}hotmail.com, Monica M. Sheffer monica.sheffer{at}uni-greifswald.de, Moritz Sonnewald moritz.sonnewald{at}senckenberg.de, Maria A. Nilsson maria.nilsson-janke{at}senckenberg.de, Axel Janke axel.janke{at}senckenberg.de * List of abbreviations BLASTN Basic Local Alignment Search Tool (for nucleotides) bp base pairs BUSCO Benchmarking Universal Single-Copy Orthologs DNBSeq DNA NanoBall sequencing Gbp Gigabase pairs hmwDNA high molecular weight DNA kbp kilobase pairs Mbp megabase pairs numt nuclear mitochondrial DNA ONT Oxford Nanopore Technologies pg picogram PI propidium iodide RNAseq RNA sequencing

Ansell's mole-rat (Fukomys anselli) is an African rodent known for its subterranean lifestyle and unique phenotypic traits, including extreme longevity, magnetoreception, and a cooperative breeding social structure. Efforts to dissect the genetic architecture of these traits and to decipher their phylogenetic relationships within the broader African mole-rat family would greatly benefit from a reference-grade genome. Here, we report a first genome assembly of a male Ansell's mole-rat. By combining Oxford Nanopore Technologies long reads and Illumina short reads with Hi-C data, we generated a chromosome level assembly with a total length of 2.27 Gb, 412 scaffolds, and a scaffold N50 of 72.4 Mb. We identified 99.54% of expected genes and annotated 29,094 transcripts using RNA sequencing data. This high-quality de novo genome of F. anselli lays the foundation for dissecting the genetic and evolutionary basis of its extraordinary traits and resolving African mole-rat phylogeny.

Ansell’s mole-rat (Fukomys anselli) is an African rodent known for its subterranean lifestyle and unique phenotypic traits, including extreme longevity, magnetoreception, and a cooperative breeding social structure. Efforts to dissect the genetic architecture of these traits and to decipher their phylogenetic relationships within the broader African mole-rat family would greatly benefit from a reference-grade genome. Here, we report a first genome assembly of a male Ansell’s mole-rat. By combining Oxford Nanopore Technologies (ONT) long-reads and Illumina short-reads with Hi-C data, we generated a chromosome level assembly with a total length of 2.27 Gb, 412 scaffolds and a scaffold N50 of 72.4 Mb. We identified 99.54% of expected genes and annotated 29,094 transcripts using RNA sequencing data. This high-quality de novo genome of Fukomys anselli lays the foundation for dissecting the genetic and evolutionary basis of its extraordinary traits and resolving African mole-rat phylogeny. Bekavac, Coimbra, and Busa et al. assemble a de novo genome of a male Fukomys anselli individual. They use short-read and long-read whole genome sequencing and Hi-C sequencing to achieve chromosome-level contiguity, and annotate the genome using RNA-seq from nine diverse tissues. This high-quality genome enables exploration of the genetic basis of Ansell’s mole-rat’s remarkable traits, including longevity, hypoxia tolerance, and magnetoreception. It also allows for comprehensive analysis of the currently-contested phylogenetic relationships within the mole-rat family.