uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Lamichhaney, SangeetORCID iD iconorcid.org/0000-0003-4826-0349
Publications (10 of 12) Show all publications
Lamichhaney, S., Han, F., Webster, M. T., Grant, B. R., Grant, P. R. & Andersson, L. (2019). Female-biased gene flow between two species of Darwin’s finches.
Open this publication in new window or tab >>Female-biased gene flow between two species of Darwin’s finches
Show others...
2019 (English)In: Article in journal (Refereed) Submitted
Abstract [en]

The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major two species of Darwin’s finches, Geospiza fortis and G. scandens, hybridize rarely and backcross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole genome sequences to compare genomes from periods before and after successful interbreeding followed by backcrossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci reflects female-biased gene flow, arising from hybrid male disadvantage in competition for territories and mates, rather than from genetic incompatibilities at Z-linked loci.

Keywords
Darwin's finches, introgression, hybridisation
National Category
Ecology Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-396776 (URN)
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28
Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R. & Grant, P. R. (2018). Rapid hybrid speciation in Darwin's finches. Science, 359(6372), 224-228
Open this publication in new window or tab >>Rapid hybrid speciation in Darwin's finches
Show others...
2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6372, p. 224-228Article in journal (Refereed) Published
Abstract [en]

Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example, from its origin to reproductive isolation. An immigrant Darwin's finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breeding with a resident finch (Geospiza fortis). Genome sequencing of the immigrant identified it as a G. conirostris male that originated on Española >100 kilometers from Daphne Major. From the second generation onward, the lineage bred endogamously and, despite intense inbreeding, was ecologically successful and showed transgressive segregation of bill morphology. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-340986 (URN)10.1126/science.aao4593 (DOI)000419816600048 ()29170277 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28
Han, F., Lamichhaney, S., Grant, B. R., Grant, P. R., Andersson, L. & Webster, M. T. (2017). Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches. Genome Research, 27(6), 1004-1015
Open this publication in new window or tab >>Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Show others...
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 6, p. 1004-1015Article in journal (Refereed) Published
Abstract [en]

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-340985 (URN)10.1101/gr.212522.116 (DOI)000402521400011 ()28442558 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28Bibliographically approved
Lamichhaney, S., Fuentes-Pardo, A. P., Rafati, N., Ryman, N., McCracken, G. R., Bourne, C., . . . Andersson, L. (2017). Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proceedings of the National Academy of Sciences of the United States of America, 114(17), E3452-E3461
Open this publication in new window or tab >>Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean
Show others...
2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 17, p. E3452-E3461Article in journal (Refereed) Published
Abstract [en]

Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5' end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2017
Keywords
genetic adaptation, Atlantic herring, parallel evolution, reproductive strategies, whole-genome resequencing
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-322174 (URN)10.1073/pnas.1617728114 (DOI)000399995600010 ()28389569 (PubMedID)
Funder
Swedish Research Council, 80576801 70374401 RGPIN-2014-04696Swedish Research Council Formas
Available from: 2017-05-17 Created: 2017-05-17 Last updated: 2017-05-17Bibliographically approved
Lamichhaney, S., Han, F., Berglund, J., Wang, C., Sällman Almen, M., T. Webster, M., . . . Andersson, L. (2016). A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science, 352(6284), 470-474
Open this publication in new window or tab >>A beak size locus in Darwin’s finches facilitated character displacement during a drought
Show others...
2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed) Published
Abstract [en]

Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

National Category
Genetics and Breeding
Identifiers
urn:nbn:se:uu:diva-279968 (URN)10.1126/science.aad8786 (DOI)000374479700050 ()27102486 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2019-11-28Bibliographically approved
Almén, M. S., Lamichhaney, S., Berglund, J., Grant, B. R., Grant, P. R., Webster, M. T. & Andersson, L. (2016). Adaptive radiation of Darwin's finches revisited using whole genome sequencing. Bioessays, 38(1), 14-20
Open this publication in new window or tab >>Adaptive radiation of Darwin's finches revisited using whole genome sequencing
Show others...
2016 (English)In: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 38, no 1, p. 14-20Article in journal (Refereed) Published
Abstract [en]

We recently used genome sequencing to study the evolutionary history of the Darwin's finches. A prominent feature of our data was that different polymorphic sites in the genome tended to indicate different genetic relationships among these closely related species. Such patterns are expected in recently diverged genomes as a result of incomplete lineage sorting. However, we uncovered conclusive evidence that these patterns have also been influenced by interspecies hybridisation, a process that has likely played an important role in the radiation of Darwin's finches. A major discovery was that segregation of two haplotypes at the ALX1 locus underlies variation in beak shape among the Darwin's finches, and that differences between the two haplotypes in a 240 kb region in blunt and pointed beaked birds involve both coding and regulatory changes. As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity.

Keywords
adaptation, evolution, gene flow, genome sequencing
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-282647 (URN)10.1002/bies.201500079 (DOI)000371265200004 ()26606649 (PubMedID)
Available from: 2016-04-06 Created: 2016-04-06 Last updated: 2017-11-30Bibliographically approved
Lamichhaney, S., Fan, G., Widemo, F., Gunnarsson, U., Thalmann, D. S., Höppner, M. P., . . . Andersson, L. (2016). Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics, 48(1), 84-+
Open this publication in new window or tab >>Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
Show others...
2016 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 1, p. 84-+Article in journal (Refereed) Published
Abstract [en]

The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females(1-4). This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles(5,6). Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-274919 (URN)10.1038/ng.3430 (DOI)000367255300018 ()26569123 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 1989-2546Swedish Research Council, 1992-2685Swedish Research Council, 2013-5418Swedish Research Council, 2001-6005Swedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-01-27 Created: 2016-01-26 Last updated: 2017-11-30Bibliographically approved
Lamichhaney, S. (2016). The genetic basis for adaptation in natural populations. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>The genetic basis for adaptation in natural populations
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations.

Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci.

The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry.

This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. p. 60
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1192
Keywords
Adaptive evolution, Atlantic herring, ecological adaptation, seasonal reproduction, TSHR, Darwin’s finches, natural selection, beak, ALX1, HMGA2, ruff, lek, inversion, HSD17B2, MC1R
National Category
Genetics and Breeding
Identifiers
urn:nbn:se:uu:diva-279969 (URN)978-91-554-9502-2 (ISBN)
Public defence
2016-04-29, B41, BMC, Husargätan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2016-04-06 Created: 2016-03-06 Last updated: 2017-04-03
Martínez Barrio, Á., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., . . . Andersson, L. (2016). The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLIFE, 5, Article ID e12081.
Open this publication in new window or tab >>The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Show others...
2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed) Published
Abstract [en]

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

National Category
Genetics and Breeding Evolutionary Biology Genetics Fish and Aquacultural Science
Identifiers
urn:nbn:se:uu:diva-279967 (URN)10.7554/eLife.12081 (DOI)000387459700001 ()27138043 (PubMedID)
Funder
EU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation
Note

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan and Nima Rafati contributed equally to this work.

Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-11-29Bibliographically approved
Saenko, S. V., Lamichhaney, S., Barrio, A. M., Rafati, N., Andersson, L. & Milinkovitch, M. C. (2015). Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Scientific Reports, 5, Article ID 17118.
Open this publication in new window or tab >>Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene
Show others...
2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 17118Article in journal (Refereed) Published
Abstract [en]

The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11th intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.

National Category
Biochemistry and Molecular Biology Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-269968 (URN)10.1038/srep17118 (DOI)000365194000001 ()26597053 (PubMedID)
Available from: 2015-12-19 Created: 2015-12-19 Last updated: 2018-01-10Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-4826-0349

Search in DiVA

Show all publications