Molecular data reveal a complex population genetic structure for <i>Psalidodon scabripinnis</i> (Teleostei: Characidae) in the Atlantic Rainforest, Brazil

Limeira, Daniel Meneguello; Santos, Mateus Henrique; Mateus, Rogério Pincela; Ruas, Claudete de Fátima; Almeida, Mara Cristina de; Moreira Filho, Orlando; Artoni, Roberto Ferreira

doi:10.1590/1678-4685-GMB-2021-0048

Daniel Meneguello Limeira

Instituto Federal do Paraná, Londrina, PR, Brazil.

http://orcid.org/0000-0001-7987-8948

Mateus Henrique Santos

Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural Molecular e Genética, Laboratório de Genética Evolutiva, Ponta Grossa, PR, Brazil.

Rogério Pincela Mateus

Universidade Estadual do Centro-Oeste, Departamento de Ciências Biológicas, Laboratório de Genética e Evolução, Guarapuava, PR, Brazil.

http://orcid.org/0000-0001-7874-1149

Claudete de Fátima Ruas

Universidade Estadual de Londrina, Departamento de Biologia Geral, Laboratório de Marcadores Moleculares e Citogenética de Plantas, Londrina, PR, Brazil.

Mara Cristina de Almeida

Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural Molecular e Genética, Laboratório de Genética Evolutiva, Ponta Grossa, PR, Brazil.

Orlando Moreira Filho

Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética e Biodiversidade, São Carlos, SP, Brazil.

Roberto Ferreira Artoni

Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural Molecular e Genética, Laboratório de Genética Evolutiva, Ponta Grossa, PR, Brazil.

http://orcid.org/0000-0002-2528-9846

Send correspondence to
Daniel Meneguello Limeira. Instituto Federal do Paraná, Av. da Liberdade, B1, Lote 26, Gleba Jacutinga, 86077-080, Londrina, PR, Brazil. E-mail: daniel.limeira@ifpr.edu.br.

Associate Editor:

Vera Maria Fonseca de Almeida e Val

Conflict of Interest

The authors declare that there is not confict of interest concerning to this paper.

Author Contributions

DM, RFA and OMF conceived the study; DML and CFR conducted the experiments with microsatellites; DML, RFA e MHS conducted the experiments with mitochondrial data; DML, RFA, MHS, MCA and RPM analyzed the data; DML wrote the manuscript; RFA, MHS and RPM revised the manuscript; all authors read and approved the final version.

Figures (2)
Tables (5)

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Figure 1 -
Collection sites for the examples of Psalidodon scabripinnis. Above and to the left, the Paraná River and Paraíba do Sul River basins; the black dot represents the collection area. Below and to the left, a specimen of Psalidodon scabripinnis. Above and to the right, approximation to the collection points and the hydrographic network; below and to the right, approximation of the collection sites, showing the altitude of each site.

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Figure 2 -
Results of the genetic structuring analysis of five Psalidodon scabripinnis populations in the Sapucaí and Paraíba do Sul basins. Above, paired F_ST (narrow arrows) and migration rate (m_{i → j}, broad arrows) for the five populations. The thickness of the arrows is proportional to the migration rate. Non-significant values for the migration rate are not shown (P < 0.05, for all values of F_ST). Below, STRUCTURE results with the three runs (a: CP+PE+RG+LV+RP; b: PE+RG+LV; c: PE+RG).

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Table 1 -
Locations, population codes, municipalities, geographic coordinates of collection points, and voucher numbers (tumble number) of ichthyology/zoology museums.

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Table 2 -
Genetic diversity parameters of five Psalidodon scabripinnis populations in the Sapucaí and Paraíba do Sul River basins, Serra da Mantiqueira region.

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Table 3 -
Values of the genetic variation of three markers (Microsatellites, COI, and ATPase) obtained through AMOVA under two hypotheses of hierarchical data (Sapucaí and Paraíba do Sul Basins and groups - PE+LV+RG, CP, and RP).

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Table 4 -
Effective population sizes (Ne) provided by the MIGRATE program and probabilities of the Wilcoxon test (P_WT), according to the two-phased mutation model (TPM), to test the heterozygosity excess, provided by the BOTTLENECK program, for five populations of Psalidodon scabripinnis from the Serra da Mantiqueira region.

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Table 5 -
Values of genetic diversity and selective neutrality test of ATPase and COI for five populations of Psalidodon scabripinnis from the Serra da Mantiqueira region.

Location/Population code	Municipalities	N	Geographic coordinates	Elevation	Voucher number
Córrego das Pedras / CP	Campos do Jordão/SP	36	22^o43’33.2’’S 45^o33’7.40’’W	1619 m	MZUEL 5655
Córrego Perdizes / PE	Campos do Jordão/SP	30	22^o44’35.3’’S 45^o34’11.6’’W	1638 m	NUP 17484
Lago Capivari / LC	Campos do Jordão/SP	30	22^o43’02.8’’S 45^o33’51.9’’W	1558 m	NUP 17486
Ribeirão Grande / RG	Pindamonhangaba/SP	21	22^o46’57.38’’S 45^o26’33.80’’W	921 m	MZUEL 5656
Córrego Lavrinhas / LV	Guaratinguetá/SP	35	22^o40’46.8’’S 45^o23’33.2’’W	1863 m	NUP 17482
Ribeirão Pequeno / RP	Pindamonhangaba /SP	26	22^o52’13.75”S 45^o35’43.51”W	606 m

	Pop	Locus	N	N_A	N_E	A_R	N_AP	H_O	H_E	F_IS
Sapucaí-Grande-Paraná River Basin
	CP	Asty21	30	12	6.977	7.662	6	0.733	0.857	0.144	^*
		Asty23	33	11	4.829	7.268	2	0.727	0.793	0.083
		Asty26	26	5	4.147	4.290	-	0.769	0.759	-0.014
		Asty27	15	7	5.488	5.707	2	0.600	0.818	0.266	^*
		Asty12	16	7	5.12	5.970	2	0.688	0.805	0.146
		Asty04	20	17	12.121	9.941	13	0.5	0.918	0.455	^*
		M/Ƹ		9.833	6.447	6.806	25	0.670	0.825	0.180
	PE	Asty21	23	7	4.921	6.493	-	0.696	0.797	0.127
		Asty23	30	4	2.975	3.557	-	0.767	0.664	-0.155
		Asty26	30	4	2.507	3.326	-	0.467	0.601	0.224
		Asty27	11	4	3.227	3.333	-	0.545	0.690	0.210	^*
		Asty12	23	5	3.752	4.621	-	0.696	0.733	0.052
		Asty04	13	5	3.756	4.824	-	0.615	0.734	0.161
		M/Ƹ		4.833	3.523	4.359	-	0.631	0.703	0.103
Paraíba do Sul River Basin
	RG	Asty21	21	6	4.594	5.379	-	0.81	0.782	-0.035
		Asty23	21	5	3.279	3.952	-	0.714	0.695	-0.028
		Asty26	21	4	2.602	3.801	-	0.524	0.616	0.149
		Asty27	5	4	3.333	3.598	1	0.2	0.7	0.714
		Asty12	17	6	4.587	5.458	-	0.647	0.782	0.173
		Asty04	13	5	3.756	4.666	-	0.538	0.734	0.266
		M/Ƹ		5	3.692	4.476	1	0.572	0.718	0.207
	LV	Asty21	26	9	6.259	7.128	-	0.692	0.84	0.176
		Asty23	22	9	4.99	6.660	-	0.636	0.8	0.204
		Asty26	35	3	1.514	2.822	-	0.286	0.34	0.159
		Asty27	8	4	3.282	3.429	-	0.625	0.695	0.101
		Asty12	13	5	3.314	4.479	-	0.615	0.698	0.119
		Asty04	23	5	2.612	4.002	-	0.522	0.617	0.155
		M/Ƹ		5.833	3.662	4.753	-	0.563	0.665	0.152
	RP	Asty21	19	5	3.455	4.459	-	0.632	0.711	0.111
		Asty23	25	9	3.858	6.173	1	0.84	0.741	-0.134
		Asty26	25	6	2.358	4.780	3	0.52	0.576	0.097
		Asty27	14	5	3.469	4.044	-	0.643	0.712	0.097
		Asty12	17	9	5.402	6.608	3	0.706	0.815	0.134
		Asty04	26	3	2.058	2.385	1	0.846	0.514	-0.646	^*
		M/Ƹ		6.167	3.433	4.742	8	0.698	0.678	-0.057

	Hierarchization of basins			Hierarchization of groups
	SSRs	COI	ATPase	SSRs	COI	ATPase
Between groups/basins	1.49	-7.44	-15.84	7.48	67.59	65.31
Among populations within groups/basins	8.529	53.27	67.00	3.70	-10.03	-1.17
Among populations	89.99	54.17	48.84	88.82	42.45	35.86
	Hierarchization of basins			Hierarchization of groups
F_CT	0.01490	-0.07441	-0.15835	0.07478	0.67585	0.65315
F_SC	0.08649^*	0.49583^*	0.57839^*	0.04005	-0.30952	-0.03383
F_ST	0.10010^*	0.45831^*	0.51162^*	0.11183^*	0.57552^*	0.64141^*

	Effective population size	Heterozygosity Excess
Pop	Ne	P_WT (TPM)
CP	33.7	0.578125
PE	10.7	0.007813
RG	16.9	0.007813
LV	33.5	0.921875
RP	2.9	0.921875

	ATPase					COI
Pop	N	h	π	D	Fs	N	h	π	D	Fs
CP	4	0	0	0	0	4	0	0	0	0
PE	5	0.6 0.1753	0.0007 0.0007	1.2247	0.6262	5	0	0	0	0
LV	4	0	0	0	0	3	0	0	0	0
RP	4	0.8333 0.2224	0.0046 0.0035	-0.4464	1.2253	3	0.4 0.2373	0.0037 0.0029	-1.1455	3.0225
RG	5	0.8 0.1640	0.0013 0.0012	0.2431	-0.4754	5	0	0	0	0

[1] Send correspondence to
Daniel Meneguello Limeira. Instituto Federal do Paraná, Av. da Liberdade, B1, Lote 26, Gleba Jacutinga, 86077-080, Londrina, PR, Brazil. E-mail: daniel.limeira@ifpr.edu.br.

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Molecular data reveal a complex population genetic structure for Psalidodon scabripinnis (Teleostei: Characidae) in the Atlantic Rainforest, Brazil

Abstract