Publications
2024
S Ebdon, DR Laetsch, R Vila, SJE Baird, K Lohse. Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies. bioRxiv, 2024.06. 03.597101
L Yusuf, K Lohse, DR Laetsch, M Ritchie. Genomic analyses in Drosophila do not support the classic allopatric model of speciation. bioRxiv, 2024.05. 20.595063
T Decroly, R Vila, K Lohse, A Mackintosh. Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence. bioRxiv, 2024.01. 20.576444
S Stankowski et al. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society 3 (1), kzae001
N Poikela, DR Laetsch, V Hoikkala, K Lohse, M Kankare. Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana. Genome Biology and Evolution, evae024
2023
A Mackintosh, PMG de la Rosa, SH Martin, K Lohse, DR Laetsch. Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny. bioRxiv
D Setter. Breakups and Hookups: a Markov model for karyotype evolution. bioRxiv
A Mackintosh, R Vila, SH Martin, D Setter, K Lohse. Do chromosome rearrangements fix by genetic drift or natural selection? A test in Brenthis butterflies. Molecular Ecology
DR Laetsch, G Bisschop, SH Martin, S Aeschbacher, D Setter, K Lohse. Demographically explicit scans for barriers to gene flow using gIMble. PLoS Genetics 19(10): e1010999
N Poikela, DR Laetsch, M Kankare, A Hoikkala, K Lohse. Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromsome. Molecular Ecology 32 (4), 854-866
A Mackintosh, R Vila, DR Laetsch, A Hayward, SH Martin, K Lohse. Chromosome Fissions and Fusions Act as Barriers to Gene Flow between Brenthis Fritillary Butterflies. Molecular Biology and Evolution 40 (3), msad043
2022
NP Poikela, DR Laetsch, K Lohse, M Kankare. Ancestrally polymorphic chromosomal inversions as potential drivers of speciation. bioRxiv
Bisschop G. 2022. Graph-based algorithms for Laplace transformed coalescence time distributions. PLoS Computational Biology 18(9): e1010532.
Setter D, Ebdon S, Jackson B, Lohse K. 2022. Estimating the rates of crossover and gene conversion from individual genomes. Genetics, iyac100
A Mackintosh, DR Laetsch, T Baril, S Ebdon, P Jay, R Vila, A Hayward, K Lohse. The genome sequence of the scarce swallowtail, Iphiclides podalirius. G3 12 (9), jkac193
Mackintosh A, Laetsch DR, Baril T, Foster RG, Dincă V, Vila R, Hayward A, Lohse K. 2022. The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome. G3 12 (6), jkac069
Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, ... Lohse K, ... Kelleher J. 2022. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 220 (3), iyab229
2021
Walton W, Stone GN, Lohse K. 2021. Discordant Pleistocene population size histories in a guild of hymenopteran parasitoids. Molecular Ecology, 30 (18): 4538-4550
Bisschop G, Lohse K, Setter D. 2021. Sweeps in time: leveraging the joint distribution of branch lengths. Genetics, 219 (2), iyab119
Ebdon S, Laetsch DR, Dapporto L, Hayward A, Ritchie MG, Dincӑ V, Vila R, Lohse K. 2021. The Pleistocene species pump past its prime: Evidence from European butterfly sister species. Molecular Ecology, 30 (14): 3575-3589
2020
Bisschop G, Setter D, Rafajlović M, Baird SJE, Lohse K. 2020. The impact of global selection on local adaptation and reproductive isolation. Philosophical Transactions of the Royal Society B 375 (1806), 20190531
Cooper L, Bunnefeld L, Hearn J, Cook K, James M, Lohse K, Stone GN. 2020. Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp. Molecular Ecology, 29: 3649– 3666
Kelleher J, Lohse K. 2020. Coalescent simulation with msprime. Statistical Population Genomics, 191-230
2019
Mackintosh A, Laetsch DR, Hayward A, Charlesworth B, Waterfall M, Vila R, Lohse K. 2019. The determinants of genetic diversity in butterflies. Nature communications 10 (1), 1-9
Kolora SRR, Weigert A, Saffari A, Kehr S, Maria Beatriz Walter Costa, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M. 2019. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. GigaScience, 8 (2), giy160
2018
Beeravolu CR, Hickerson MJ, Frantz LAF, Lohse K. 2019. ABLE: blockwise site frequency spectra for inferring complex population histories and recombination. Genome biology 19 (1), 1-16
Bunnefeld L, Hearn J, Stone GN , Lohse K. 2018. Whole-genome data reveal the complex history of a diverse ecological community. PNAS
Jordan CY, Lohse K, Turner F, Thomson M, Gharbi K, Ennos RA. 2018. Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems. Molecular Ecology, 27: 1214-1228
2017
Lohse K. 2017. Come on feel the noise – from metaphors to null models. JEB , 30 (8), 1506–1508
2016
Nuernberger B, Lohse K, Fijarczyk A, Szymura, JM, Blaxter M. 2016. Para-allopatry in hybridizing fire-bellied toads (Bombina bombinaand B. variegata): inference from transcriptome-wide coalescence analyses, Evolution, 70 (8): 1803–1818
Lohse K, Chmelik M, Martin SH, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent, Genetics, 202 (2): 775-786
2015
Lohse K, Ross L. 2015. What haplodiploids can teach us about hybridization and speciation, Molecular Ecology, 4 (20): 5075-5077
Bunnefeld L, Frantz LAF, Lohse K. 2015. Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks, Genetics, 201 (3): 1157-1169
Lohse K, Clarke M, Ritchie MG, Etges WJ. 2015. Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation, Evolution, 69 (5): 1178–1190
2014
Frantz LAF, Madsen O, Megens H-J, Groenen MAM, Lohse K. 2014. Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations, Molecular Ecology, 23(22): 5566–5574
Lohse K, Frantz LAF. 2014. Maximum likelihood evidence for Neandertal admixture in Eurasia from three genome. Genetics 196 (4): 1241-1251
Hearn J, Stone GN, Nicholls JA, Barton N, Lohse K. 2014. Likelihood-based inference of population history from low coverage de novo genome assemblies, Molecular Ecology, 23 (1): 198-211
2013
Melika G, Tang C-T, Sinclair F, Yang M-M, Lohse K, Hearn J, Nicholls JA, Stone GN. 2013. A new genus of oak gallwasp, Cyclocynips Melika, Tang & Sinclair (Hymenoptera: Cynipidae, Cynipini), with descriptions of two new species from Taiwan, Zootaxa , 3630 (3): 534-548
2012
Lohse K, Barton N, Melika G, Stone GN. 2012. A likelihood based comparison of population histories in a parasitoid guild, Molecular Ecology, 22(18): 4605-4617
Smith G, Lohse K, Etges WJ, Ritchie MG. 2012. Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis, Molecular Ecology, 21: 3293-3307
Stone* GN, Lohse* K, Nicholls JA, Sinclair F, Schönrogge K, Csóka G, Melika G, Nieves-Aldrey J-N, Pujade-Villar J, Tavakoli M, Askew RR, Hickerson* MJ. 2012. Reconstructing community assembly in time and space reveals enemy escape in a western Palearctic insect community, Current Biology, 22 (6), R182-183
2011
Lohse K, Harrison R, Barton N. 2011. A general method for calculating likelihoods under the coalescent process, Genetics, 189 (3): 977-987
Lohse K, Sharanowski B, Blaxter M, Nicholls JA, Stone GN. 2011. Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data. Molecular Ecology Resources, 11, 521-529
Lohse K, Nicholls JA, Stone GN. 2011. Inferring the colonisation of a mountain range – nunatak survival in high alpine ground beetles. Molecular Ecology, 20: 394-408
2010
Lohse K, Sharanowski B, Stone GN. 2010. Quantifying the Pleistocene history of the oak gall parasitoid Cecidostiba fungosa using twenty intron loci. Evolution, 64 (9): 2664-2681
Kaatinen R, Stone GN, Hearn J, Lohse K, Roslin T. 2010. Revealing secret liaisons: DNA bar-coding changes our understanding of food webs. Entomologial Ecology, 35 (5): 623-638
2009
Lohse K. 2009. Can barcodes be used to delimit species? A response to Pons et al. (2006). Systematic Biology, 58 (4): 439-442
Lohse K, Kelleher J. 2009. Measuring the degree of starshape in genealogies – summary statistics and demographic inference. Genetics Research, 91: 281-292
2007
Lohse K, Gutierrez A, Kaltz O. 2007. Experimental evolution of resistance in Paramecium caudatum against the bacterial parasite Holospora undulata. Evolution, 60 (6): 1177-1186