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Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

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145 days ago
RT @airdrian: New #preprint: Octopus life history predicts genetics in Northwest Mexico https://t.co/pehCzVuxpt #OpenAccess
Octopus life history predicts genetics https://t.co/Tw9KKX804L
165 days ago
New #preprint: Octopus life history predicts genetics in Northwest Mexico https://t.co/pehCzVuxpt #OpenAccess
165 days ago
Life histories predict genetic diversity and population structure within three species of Octopus targeted by… https://t.co/tDd1mqyCeh
peerJ: Life histories predict genetic diversity and population structure within three species of Octopus targeted… https://t.co/yTL1fsD6pj
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Supplemental Information

Hardy-Weinberg equilibrium

Tests of Hardy-Weinberg equilibrium in 20 populations of octopus genotyped at 7 loci. Estimation of exact P-values by the Markov chain method. Parameters: 10,000 dememorization, 1000 batches and 10,000 iterations per batch.

DOI: 10.7287/peerj.preprints.3016v2/supp-1

Null allele frequency

Average null allele frequency obtained with FREENA using Expectation Maximization algorithm of Dempster in 20 populations of octopus genotyped at 7 loci.

DOI: 10.7287/peerj.preprints.3016v2/supp-2

Correction for null alleles

Correction of FST with and without null alleles estimated with FREENA. Confidence intervals (CI) calculated using 10,000 bootstraps.

DOI: 10.7287/peerj.preprints.3016v2/supp-3

Genetic differentiation of Octopus bimaculoides

Genetic differentiation between pairs of localities for Octopus bimaculoides. FST values below the diagonal and F’ST above diagonal.

DOI: 10.7287/peerj.preprints.3016v2/supp-4

Genetic differentiation of Octopus hubbsorum

Genetic differentiation between pairs of localities for Octopus hubbsorum. FST below the diagonal significance in bold. F'ST above the diagonal. Shadow area correspond to Pacific Coast.

DOI: 10.7287/peerj.preprints.3016v2/supp-5

Genetic differentiation of Octopus bimaculatus

Genetic differentiation between pairs of localities for Octopus bimaculatus. FST below the diagonal. Significance in bold. F'ST above the diagonal. Shadow area correspond to Pacific Coast.

DOI: 10.7287/peerj.preprints.3016v2/supp-6

Structure clustering algorithm

Structure clustering algorithm: A) Delta K is the mean of the absolute values, B) mean and standard deviation of Ln probability of data for No. of genetic cluster (K) =1 to 20 and C) bar plot showing the mean individual assignment probabilities among 10 independent replicates of both K = 2 and K = 3.

DOI: 10.7287/peerj.preprints.3016v2/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

José F Domínguez-Contreras conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Adrian Munguia-Vega conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Bertha P Ceballos-Vázquez contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Marcial Arellano-Martínez contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Francisco J García-Rodríguez contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Melanie Culver contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Héctor Reyes-Bonilla contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field experiments were approved by Secretaria de Agricultura, Ganaderia, Desarrollo Rural, Pesca y Alimentación (SAGARPA).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The COI and 16S rDNA sequences described here are accessible via GenBank accession numbers KY985098 to KY985194.

Funding

Fondo Institucional CONACYT-Fronteras de la Ciencia, proyecto 26/2016. "Estudio integrativo de la biodiversidad y la conservación del Golfo de California, bajo un enfoque de paisaje genético marino y conectividad" This research was partially financed by SIP projects: 20120971, 20121594, 20130059, 20130089, 20140781, 20140465, 20150998, 20150117 and CONACyT 108230. JFDC benefited from CONACyT doctoral (328943) and postdoctoral (291053 estancias posdoctorales nacionales 2016-1) scholarships This work was partially supported via the PANGAS Science Coordination by the David and Lucile Packard Foundation grants #2013-39400, #2015- 62798. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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