title: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales.
abstract: Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information and estimated rates of gene flow using maximum-likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographical distance (IBD P < 0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broadscale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST0.034-0.161; P < 0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster and geneflow analyses. Instances of male fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. The relationships between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.
authors.affiliation: Columbia University, 116th Street and Broadway, New York, NY, 10027, USA.
authors.forename: Francine
authors.initials: F
authors.lastname: Kershaw
authors.affiliation: Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.|Centre for Environmental and Marine Studies (CESAM), Universidade de Aveiro,  Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
authors.forename: Inês
authors.initials: I
authors.lastname: Carvalho
authors.affiliation: Department of Biology, New York University, 100 Washington Square, New York, NY, 10012, USA.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Loo
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Cristina
authors.initials: C
authors.lastname: Pomilla
authors.affiliation: Mammal Research Institute, University of Pretoria, c/o Iziko South African Museum, P.O. Box 61, Cape Town, 8000, South Africa.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Best
authors.affiliation: Mammal Research Institute, University of Pretoria, c/o Iziko South African Museum, P.O. Box 61, Cape Town, 8000, South Africa.
authors.forename: Ken P
authors.initials: KP
authors.lastname: Findlay
authors.affiliation: Wildlife Conservation Society, Ocean Giants Program, 2300 Southern Blvd., Bronx, NY, 10460-1099, USA.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Cerchio
authors.affiliation: Wildlife Conservation Society, Ocean Giants Program, 2300 Southern Blvd., Bronx, NY, 10460-1099, USA.|Environment Society of Oman, P.O. Box 3955, PC 112, Ruwi, Sultanate of Oman.
authors.forename: Tim
authors.initials: T
authors.lastname: Collins
authors.affiliation: Humpback Whale Project/Humpback Whale Institute, Rua Barão do Rio Branco, 125, Caravelas, Bahia, Brazil.
authors.forename: Marcia H
authors.initials: MH
authors.lastname: Engel
authors.affiliation: Environment Society of Oman, P.O. Box 3955, PC 112, Ruwi, Sultanate of Oman.
authors.forename: Gianna
authors.initials: G
authors.lastname: Minton
authors.affiliation: Center for Biodiversity and Conservation, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Ersts
authors.affiliation: Mammal Research Institute, University of Pretoria, c/o Iziko South African Museum, P.O. Box 61, Cape Town, 8000, South Africa.
authors.forename: Jaco
authors.initials: J
authors.lastname: Barendse
authors.affiliation: Department of Environmental Affairs, Branch Oceans and Coasts, Private Bag x2, Roggebaai 8012, Cape Town, South Africa.
authors.forename: P G H
authors.initials: PG
authors.lastname: Kotze
authors.affiliation: Wildlife Conservation Society-Madagascar Program, 2300 Southern Blvd., Bronx, NY, 10460-1099, USA.
authors.forename: Yvette
authors.initials: Y
authors.lastname: Razafindrakoto
authors.affiliation: Agence Nationale des Parcs Nationaux, Batterie 4, BP 20379, Libreville, Gabon.
authors.forename: Solange
authors.initials: S
authors.lastname: Ngouessono
authors.affiliation: Department of Environmental Affairs, Branch Oceans and Coasts, Private Bag x2, Roggebaai 8012, Cape Town, South Africa.
authors.forename: Michael
authors.initials: M
authors.lastname: Meÿer
authors.affiliation: Mammal Research Institute, University of Pretoria, c/o Iziko South African Museum, P.O. Box 61, Cape Town, 8000, South Africa.
authors.forename: Meredith
authors.initials: M
authors.lastname: Thornton
authors.affiliation: Wildlife Conservation Society, Ocean Giants Program, 2300 Southern Blvd., Bronx, NY, 10460-1099, USA.|Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
authors.forename: Howard C
authors.initials: HC
authors.lastname: Rosenbaum
mesh_terms: D000351:Africa, Eastern; D000354:Africa, Western; D000818:Animals; D001499:Bayes Theorem; D005260:Female; D000069196:Gastrointestinal Microbiome; D040342:Genetic Structures; D050640:Humpback Whale; D019156:Indian Ocean; D008116:Lizards; D008297:Male; D013019:South Africa
keywords: International Whaling Commission; Southern Hemisphere; behaviour; humpback whale; population genetics; wildlife management