Axel Janke

Axel Janke
Senckenberg Research Institute · Project Area Laboratory Centre & Spokesman LOEWE TBG

Prof. Dr.

About

185
Publications
51,090
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8,534
Citations
Additional affiliations
May 2010 - present
Goethe-Universität Frankfurt am Main
Position
  • Professor (Full)
February 2010 - July 2021
Lund University
Position
  • Professor

Publications

Publications (185)
Article
Full-text available
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 8...
Article
Full-text available
Traditionally, one giraffe species and up to eleven subspecies have been recognized [1]; however, nine subspecies are commonly accepted [2]. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies o...
Article
Full-text available
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes like incomplete lineage sorting and introg...
Article
Full-text available
The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis...
Article
Full-text available
Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes.
Article
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult...
Article
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult...
Article
Full-text available
Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the e...
Article
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It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained large...
Article
Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to...
Article
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November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phas...
Article
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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...
Article
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Like many carnivore species, European wildcats (Felis silvestris) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck at the beginning of the 20th century. In Germany, the species has managed to survive its near extinction in small isolated areas and is currently recolonizing former habita...
Preprint
Full-text available
Feeding exclusively on blood, vampire bats represent the only obligate sanguivorous lineage among mammals. To uncover genomic changes associated with adaptations to this unique dietary specialization, we generated a new haplotype-resolved reference-quality genome of the common vampire bat (Desmodus rotundus) and screened 26 bat species for genes th...
Article
Full-text available
Striking geographic variation in male advertisement calls was observed in frogs formerly referred to as Limnonectes doriae and L. limborgi, respectively. Subsequent analyses of mtDNA and external morphological data brought supporting evidence for the recognition of these populations as distinct species. We describe two new frog species of the genus...
Article
Full-text available
Background: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. Ho...
Article
Full-text available
Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s.1 However, one species with nine subspecies has been generally accepted,2 likely due to limited in-depth assessments, subspecies hybridizi...
Article
Full-text available
We revise the frogs of the genus Phrynoglossus from Indochina based on data of external morphology, bioacoustics and molecular genetics. The results of this integrative study provide evidence for the recognition of three distinct species, one of which we describe as new. Phrynoglossus martensii has a vast geographic distribution from central and so...
Article
Full-text available
We revise the frogs of the genus Phrynoglossus from Indochina based on data of external morphology, bioacoustics and molecular genetics. The results of this integrative study provide evidence for the recognition of three distinct species, one of which we describe as new. Phrynoglossus martensii has a vast geographic distribution from central and so...
Article
SNP data sets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time-consuming and challenging process, not in the least because at present many different software packages are needed to...
Article
Based on two male and two female individuals, we describe a new genus and species of mud snake, Myanophis thanlyinensis gen. nov., sp. nov., from the vicinity of the campus of East Yangon University, Yangon, Thanlyin, Myanmar. This species differs from every other homalopsid species by the following combination of characters: (1) dorsal scales smoo...
Chapter
Bears have fascinated people since ancient times. The relationship between bears and humans dates back thousands of years, during which time we have also competed with bears for shelter and food. In modern times, bears have come under pressure through encroachment on their habitats, climate change, and illegal trade in their body parts, including t...
Article
Full-text available
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. Callio...
Preprint
Full-text available
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. Calli...
Preprint
Full-text available
Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in evolutionary sciences, ecology, systematics and in biodiversity-related applied fields such as environmental management and natural product research. Advances in DNA sequencing technologies make genome sequencing feasible for many non-genetic model species. Howeve...
Article
Wastewater-based monitoring of the spread of the new SARS-CoV-2 virus, also referred to as wastewater-based epidemiology (WBE), has been suggested as a tool to support epidemiology. An extensive sampling campaign, including nine municipal wastewater treatment plants, has been conducted in different cities of the Federal State of North Rhine-Westpha...
Preprint
Full-text available
Background: SNP datasets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time-consuming and challenging process, not in the least because at present many different software packages ar...
Article
Full-text available
Recent advances in genome sequencing technologies have simplified the generation of genome data and reduced the costs for genome assemblies, even for complex genomes like those of vertebrates. More practically oriented genomic courses can prepare university students for the increasing importance of genomic data used in biological and medical resear...
Article
Full-text available
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 mast...
Preprint
Full-text available
Background 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 univ...
Article
Full-text available
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 assume...
Article
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Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is narrowly sympatric with each of t...
Article
Full-text available
All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analys...
Preprint
Full-text available
All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analys...
Article
Full-text available
Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a...
Article
The distribution maps of giraffe (Giraffa) subspecies in southern Africa are based on historical assumptions, yet some populations have likely been misidentified, hindering effective conservation efforts. Particularly, the populations in Zimbabwe are poorly studied, and translocations, such as the 1991 movement of giraffe from Namibia's Etosha Nati...
Article
Full-text available
Background: We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically...
Article
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact...
Article
Full-text available
Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high throughput seque...
Article
Full-text available
Phylogenetic analyses of nuclear and mitochondrial genomes indicate that polar bears captured the brown bear mitochondrial genome 160,000 years ago, leading to an extinction of the original polar bear mitochondrial genome. However, mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochond...
Preprint
Full-text available
Compared to sequence analyses, phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear spec...
Article
Full-text available
It is not unexpected that a proposal, such as ours [1] , of four new mammalian species stirs up controversy, as evident in the correspondence by Bercovitch et al. [2] . We appreciate that their concerns are unrelated to the quality of the genetic data, the methodological approach or analyses, but are focused on the interpretation. Thus, we provided...
Article
Full-text available
Here we present an approach to establish species-specific genetic markers for sex identification suitable for non-invasive samples. Such markers are not yet available for the endangered common hamster (Cricetus cricetus) because of the lack of genomic resources. Using Y chromosome conserved anchored tagged sequences (YCATS) exonic primers, we obtai...
Preprint
Full-text available
Phylogenetic analyses of nuclear and mitochondrial genomes have shown that polar bears captured the mitochondrial genome of brown bears some 160,00 years ago. This hybridization event likely led to an extinction of the original polar bear mitochondrial genome. However, parts of the mitochondrial DNA occasionally integrates into the nuclear genome,...
Preprint
Full-text available
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to the closely related polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylog...
Article
Full-text available
Projections by the Intergovernmental Panel on Climate Change (IPCC) and sea ice forecasts suggest that Arctic sea ice will decline markedly in coming decades. Expected effects on the entire ecosystem include a contraction of suitable polar bear habitat into one or few refugia. Such large-scale habitat decline and fragmentation could lead to reduced...
Article
High-resolution, male-inherited Y-chromosomal markers are a useful tool for population genetic analyses of wildlife species, but to date have only been applied in this context to relatively few species besides humans. Using nine Y-chromosomal STR and three Y-chromosomal single nucleotide polymorphism markers (Y-SNPs), we studied whether male gene f...
Article
Full-text available
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent model in phylogenomics, popularly known as “species tree” methods. After pointing out errors in alignments and gene tree rooting in recent phyloge...