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Items: 35

1.

The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography.

Lado S, Alves PC, Islam MZ, Brito JC, Melo-Ferreira J.

Heredity (Edinb). 2019 Nov;123(5):634-646. doi: 10.1038/s41437-019-0229-8. Epub 2019 May 9.

PMID:
31073237
2.

The genomic impact of historical hybridization with massive mitochondrial DNA introgression.

Seixas FA, Boursot P, Melo-Ferreira J.

Genome Biol. 2018 Jul 30;19(1):91. doi: 10.1186/s13059-018-1471-8.

3.

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares.

Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J, Good JM.

Science. 2018 Jun 22;360(6395):1355-1358. doi: 10.1126/science.aar5273.

PMID:
29930138
4.

Function and underlying mechanisms of seasonal colour moulting in mammals and birds: what keeps them changing in a warming world?

Zimova M, Hackländer K, Good JM, Melo-Ferreira J, Alves PC, Mills LS.

Biol Rev Camb Philos Soc. 2018 Aug;93(3):1478-1498. doi: 10.1111/brv.12405. Epub 2018 Mar 5. Review.

PMID:
29504224
5.

Winter color polymorphisms identify global hot spots for evolutionary rescue from climate change.

Mills LS, Bragina EV, Kumar AV, Zimova M, Lafferty DJR, Feltner J, Davis BM, Hackländer K, Alves PC, Good JM, Melo-Ferreira J, Dietz A, Abramov AV, Lopatina N, Fay K.

Science. 2018 Mar 2;359(6379):1033-1036. doi: 10.1126/science.aan8097. Epub 2018 Feb 15.

PMID:
29449510
6.

Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains.

Silvério D, Lopes AM, Melo-Ferreira J, Magalhães MJ, Monterroso P, Serronha A, Maio E, Alves PC, Esteves PJ, Abrantes J.

Transbound Emerg Dis. 2018 Aug;65(4):983-992. doi: 10.1111/tbed.12830. Epub 2018 Feb 11.

PMID:
29430852
7.

Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares.

Marques JP, Ferreira MS, Farelo L, Callahan CM, Hackländer K, Jenny H, Montgomery WI, Reid N, Good JM, Alves PC, Melo-Ferreira J.

Sci Data. 2017 Dec 5;4:170178. doi: 10.1038/sdata.2017.178.

8.

The transcriptional landscape of seasonal coat colour moult in the snowshoe hare.

Ferreira MS, Alves PC, Callahan CM, Marques JP, Mills LS, Good JM, Melo-Ferreira J.

Mol Ecol. 2017 Aug;26(16):4173-4185. doi: 10.1111/mec.14177. Epub 2017 Jun 7.

PMID:
28500774
9.

Range expansion underlies historical introgressive hybridization in the Iberian hare.

Marques JP, Farelo L, Vilela J, Vanderpool D, Alves PC, Good JM, Boursot P, Melo-Ferreira J.

Sci Rep. 2017 Jan 25;7:40788. doi: 10.1038/srep40788.

10.

Genetic Basis for Red Coloration in Birds.

Lopes RJ, Johnson JD, Toomey MB, Ferreira MS, Araujo PM, Melo-Ferreira J, Andersson L, Hill GE, Corbo JC, Carneiro M.

Curr Biol. 2016 Jun 6;26(11):1427-34. doi: 10.1016/j.cub.2016.03.076. Epub 2016 May 19.

11.

Endogenization of mouse mammary tumor virus (MMTV)-like elements in genomes of pikas (Ochotona sp.).

Lemos de Matos A, de Sousa-Pereira P, Lissovsky AA, van der Loo W, Melo-Ferreira J, Cui J, Esteves PJ.

Virus Res. 2015 Dec 2;210:22-6. doi: 10.1016/j.virusres.2015.06.021. Epub 2015 Jul 4.

PMID:
26151606
12.

The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach.

Melo-Ferreira J, Lemos de Matos A, Areal H, Lissovsky AA, Carneiro M, Esteves PJ.

Mol Phylogenet Evol. 2015 Mar;84:240-4. doi: 10.1016/j.ympev.2015.01.004. Epub 2015 Jan 28.

PMID:
25637497
13.

Sequencing of Sylvilagus VDJ genes reveals a new VHa allelic lineage and shows that ancient VH lineages were retained differently in leporids.

Pinheiro A, Melo-Ferreira J, Abrantes J, Martinelli N, Lavazza A, Alves PC, Gortázar C, Esteves PJ.

Immunogenetics. 2014 Dec;66(12):719-26. doi: 10.1007/s00251-014-0807-0. Epub 2014 Sep 30.

PMID:
25267061
14.

The genomic architecture of population divergence between subspecies of the European rabbit.

Carneiro M, Albert FW, Afonso S, Pereira RJ, Burbano H, Campos R, Melo-Ferreira J, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Good JM, Ferrand N.

PLoS Genet. 2014 Aug 28;10(8):e1003519. doi: 10.1371/journal.pgen.1003519. eCollection 2014 Aug.

15.

The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation.

Melo-Ferreira J, Seixas FA, Cheng E, Mills LS, Alves PC.

Mol Ecol. 2014 Sep;23(18):4617-30. doi: 10.1111/mec.12886. Epub 2014 Sep 5.

PMID:
25113393
16.

Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare.

Cheng E, Hodges KE, Melo-Ferreira J, Alves PC, Mills LS.

Mol Ecol. 2014 Jun;23(12):2929-42. doi: 10.1111/mec.12790. Epub 2014 Jun 9.

PMID:
24814937
17.

The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression.

Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC.

Genome Biol Evol. 2014 Apr;6(4):886-96. doi: 10.1093/gbe/evu059.

18.

Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?

Boratyński Z, Melo-Ferreira J, Alves PC, Berto S, Koskela E, Pentikäinen OT, Tarroso P, Ylilauri M, Mappes T.

Heredity (Edinb). 2014 Oct;113(4):277-86. doi: 10.1038/hdy.2014.28. Epub 2014 Apr 2.

19.

Advances in Ecological Speciation: an integrative approach.

Faria R, Renaut S, Galindo J, Pinho C, Melo-Ferreira J, Melo M, Jones F, Salzburger W, Schluter D, Butlin R.

Mol Ecol. 2014 Feb;23(3):513-21. doi: 10.1111/mec.12616.

PMID:
24354648
20.

Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes.

Korrodi-Gregório L, Abrantes J, Muller T, Melo-Ferreira J, Marcus K, da Cruz e Silva OA, Fardilha M, Esteves PJ.

BMC Evol Biol. 2013 Nov 6;13:242. doi: 10.1186/1471-2148-13-242.

21.

Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing.

Melo-Ferreira J, Farelo L, Freitas H, Suchentrunk F, Boursot P, Alves PC.

Heredity (Edinb). 2014 Mar;112(3):265-73. doi: 10.1038/hdy.2013.102. Epub 2013 Oct 23.

22.

Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.

Gayral P, Melo-Ferreira J, Glémin S, Bierne N, Carneiro M, Nabholz B, Lourenco JM, Alves PC, Ballenghien M, Faivre N, Belkhir K, Cahais V, Loire E, Bernard A, Galtier N.

PLoS Genet. 2013 Apr;9(4):e1003457. doi: 10.1371/journal.pgen.1003457. Epub 2013 Apr 11.

23.

Past, present and future distributions of an Iberian Endemic, Lepus granatensis: ecological and evolutionary clues from species distribution models.

Acevedo P, Melo-Ferreira J, Real R, Alves PC.

PLoS One. 2012;7(12):e51529. doi: 10.1371/journal.pone.0051529. Epub 2012 Dec 13.

24.

Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia.

Paupério J, Herman JS, Melo-Ferreira J, Jaarola M, Alves PC, Searle JB.

Mol Ecol. 2012 Dec;21(24):6015-32. doi: 10.1111/mec.12024. Epub 2012 Nov 19.

PMID:
23163319
25.

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data.

Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N.

Mol Ecol Resour. 2012 Sep;12(5):834-45. doi: 10.1111/j.1755-0998.2012.03148.x. Epub 2012 Apr 30.

PMID:
22540679
26.

Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome.

Carneiro M, Albert FW, Melo-Ferreira J, Galtier N, Gayral P, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Ferrand N.

Mol Biol Evol. 2012 Jul;29(7):1837-49. doi: 10.1093/molbev/mss025. Epub 2012 Jan 31.

27.

Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations.

Melo-Ferreira J, Boursot P, Carneiro M, Esteves PJ, Farelo L, Alves PC.

Syst Biol. 2012 May;61(3):367-81. doi: 10.1093/sysbio/syr114. Epub 2011 Dec 26.

PMID:
22201159
28.

Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?

Boratyński Z, Alves PC, Berto S, Koskela E, Mappes T, Melo-Ferreira J.

BMC Evol Biol. 2011 Dec 9;11:355. doi: 10.1186/1471-2148-11-355.

29.

Interspecific X-chromosome and mitochondrial DNA introgression in the Iberian hare: selection or allele surfing?

Melo-Ferreira J, Alves PC, Rocha J, Ferrand N, Boursot P.

Evolution. 2011 Jul;65(7):1956-68. doi: 10.1111/j.1558-5646.2011.01261.x. Epub 2011 Mar 16.

PMID:
21729051
30.

The genomic legacy from the extinct Lepus timidus to the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes.

Melo-Ferreira J, Alves PC, Freitas H, Ferrand N, Boursot P.

Mol Ecol. 2009 Jun;18(12):2643-58. doi: 10.1111/j.1365-294X.2009.04221.x. Epub 2009 May 15.

PMID:
19457181
31.

The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus.

Alves PC, Melo-Ferreira J, Freitas H, Boursot P.

Philos Trans R Soc Lond B Biol Sci. 2008 Sep 12;363(1505):2831-9. doi: 10.1098/rstb.2008.0053.

32.

Evidence for genetic similarity of two allopatric European hares (Lepus corsicanus and L. castroviejoi) inferred from nuclear DNA sequences.

Alves PC, Melo-Ferreira J, Branco M, Suchentrunk F, Ferrand N, Harris DJ.

Mol Phylogenet Evol. 2008 Mar;46(3):1191-7. doi: 10.1016/j.ympev.2007.11.010. Epub 2007 Nov 28. No abstract available.

PMID:
18178109
33.

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula.

Melo-Ferreira J, Boursot P, Randi E, Kryukov A, Suchentrunk F, Ferrand N, Alves PC.

Mol Ecol. 2007 Feb;16(3):605-18.

PMID:
17257116
34.

Hares on thin ice: introgression of mitochondrial DNA in hares and its implications for recent phylogenetic analyses.

Alves PC, Harris DJ, Melo-Ferreira J, Branco M, Ferrand N, Suchentrunk F, Melo-Ferreira J, Boursot P.

Mol Phylogenet Evol. 2006 Aug;40(2):640-1. Epub 2006 Apr 18. No abstract available.

PMID:
16624594
35.

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