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Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair

Citation

Cruz Nicolás, Jorge et al. (2021), Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair, Dryad, Dataset, https://doi.org/10.5061/dryad.sbcc2fr2x

Abstract

Aim: Estimating genetic diversity is key for understanging biogeographic and evolutionary processes. However, gathering genetic information is not feasible for all taxa or populations, particularly in the tropical regions. Identifying proxies for inferring such values has thus become essential. Here, we built on the niche centrality hypothesis (NCH; or central-abundance hypothesis) and the nearly neutral theory of evolution (NNT) to identify some of such proxies using a montane tropical conifer species-pair as model. The NCH predicts more genetic diversity under optimal ecological conditions, which should also allow for more efficient purifying selection, according to the NNT.

Location: The Transmexican Volcanic Belt, central Mexico.

Taxa: A fir species-pair endemic to central Mexico, Abies flinckii and A. religiosa.

Methods: We estimated patterns of genetic diversity from nuclear SSRs (A, HE), and gene-coding sequences (πS, πN), together with the efficacy of purifying selection, measured as πN/πS. After testing for niche overlap, we used several geographic and ecological proxies (i.e. longitude, latitude, elevation, estimated area, and distance to the niche centroid in the present and in the LGM) to predict genetic diversity and πN/πS using general linear models.

Results: Populations at the west of the Trans Mexican Volcanic Belt (TVB) had lower genetic diversity than populations in the east of this mountain chain. Both species had significant niche overlap. The principal predictors for neutral genetic diversity (HE, A and πS) were longitude and latitude, followed by the current distance to the niche centroid; the efficiency of purifying selection was mostly accounted for by the current distance to the niche centroid (which was also correlated to elevation). No correlation was observed between genetic diversity or πN/πS and current population area.

Main conclusions: Historical and ecological factors have to be taken into account for explaining the amounts of genetic diversity in mountain tropical species. Following the NTT, populations closer to the niche centroid are more efficient at eliminating slightly deleterious mutations than marginal stands, independently of their size or geographical location (longitude). Expanding the central-abundance theory within the scope of the NTT might help reconciling conflicting views concerning the extent of its empirical support.

Methods

We sampled needles for natural populations of two species Abies flinckii and A. religiosa in central Mexico. We sequenced 11 gene-coding regions with Sanger sequencing and four nucelar SSRs. The table 1 shows details (n= sample size).

Population Species n =Sequencing coding regions n= Nuclear SSRs Longitude Latitude Elevation
1 (AF14) A. flinckii 4 20 -100.75 19.583 2340
2 (AF16) A. flinckii 7 20 -101.35 19.333 2250
3 (AF17) A. flinckii 7 18 -102.95 18.767 2500
4 (AF18) A. flinckii 5 22 -104.716 20.2 2100
5(AF19) A. flinckii 7 20 -105.000 20.35 2490
6 (AF20) A. flinckii 7 20 -103.933 19.45 2500
8 (AR12) A. religiosa 7 21 -99.80 19.183 3240
9(AR13) A. religiosa 7 20 -100.18 19.433 2800
10 (AR15) A. religiosa 7 21 -100.817 19.667 2880
11 (AR21) A. religiosa 7 19 -103.95 19.45 2500
12 (AR22) A. religiosa 7 18 -103.583 19.583 3330
13 (AR45) A. religiosa 7 22 -97.35 18.967 3060
14 (AR48) A. religiosa 7 21 -97.15 19.517 3510
15 (AR49) A. religiosa 7 19 -98.083 19.683 2760
16 (AR53) A. religiosa 7 19 -98.7 20.15 2940
17 (AR54) A. religiosa 7 20 -98.683 19.083 3330
18 (AR55) A. religiosa 7 20 -102.317 19.383 3030
19 A. religiosa 7 20 -99.267 19.223 3369
20 A. religiosa   19 -98.055 19.253 3358
21 A. religiosa   20 -103.642 19.521 2928
             

 

Usage Notes

There are two files nuclear SSRs gene pop (.gen) for each species.

  1. micros_flinckii.gen (Nuclear SSRs for Abies flinckii)
  2. micros_religiosa.gen (Nuclear SSRs for Abies religiosa)

Code: A. flinckii = Abies flinckii

14 = Abies flinckii, population 1

16 = Abies flinckii, population 2

17 = Abies flinckii, population 3

18 = Abies flinckii, population 4

19 = Abies flinckii, population 5

20 = Abies flinckii, population 6

A. religiosa = Abies religiosa

12 = Abies religiosa, population 8

13 = Abies religiosa, population 9

15 = Abies religiosa, population 10

21 = Abies religiosa, population 11

22 = Abies religiosa, population 12

45 = Abies religiosa, population 13

48 = Abies religiosa, population 14

49 = Abies religiosa, population 15

53 = Abies religiosa, population 16

54 = Abies religiosa, population 17

55 = Abies religiosa, population 18

Abies religiosa, population 19

AbM = Abies religiosa population 20

Abies religiosa, population 21.

There are eleven fasta files with the alignments for each species/populations (.fas)

Thera are two files (.csv) with the occurence points used for ecological niche modellings.

Funding

Consejo Nacional de Ciencia y Tecnología, Award: CB-2016-284457

Consejo Nacional de Innovación, Ciencia y Tecnología, Award: CB-2016-278987

Universidad Nacional Autónoma de México, Award: PAPIIT-IN208416