DOI: 10.5061/dryad.sbcc2fr2x
title: Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair

description: 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.
description: We sampled needles for natural populations of two species
 <em>Abies flinckii</em> and <em>A. religiosa
 </em>in central Mexico<em>. </em>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) <em>A. flinckii</em>
 4 20
 -100.75 19.583
 2340 2
 (AF16) <em>A. flinckii</em>
 7 20
 -101.35 19.333
 2250 3
 (AF17) <em>A. flinckii</em>
 7 18
 -102.95 18.767
 2500 4
 (AF18) <em>A. flinckii</em>
 5 22
 -104.716 20.2
 2100 
 5(AF19) <em>A.
 flinckii</em> 7
 20 -105.000
 20.35 2490 
 6 (AF20) <em>A.
 flinckii</em> 7
 20 -103.933
 19.45 2500 
 8 (AR12) <em>A.
 religiosa</em> 7
 21 -99.80
 19.183 3240 
 9(AR13) <em>A.
 religiosa</em> 7
 20 -100.18
 19.433 2800 
 10 (AR15) <em>A.
 religiosa</em> 7
 21 -100.817
 19.667 2880 
 11 (AR21) <em>A.
 religiosa</em> 7
 19 -103.95
 19.45 2500 
 12 (AR22) <em>A.
 religiosa</em> 7
 18 -103.583
 19.583 3330 
 13 (AR45) <em>A.
 religiosa</em> 7
 22 -97.35
 18.967 3060 
 14 (AR48) <em>A.
 religiosa</em> 7
 21 -97.15
 19.517 3510 
 15 (AR49) <em>A.
 religiosa</em> 7
 19 -98.083
 19.683 2760 
 16 (AR53) <em>A.
 religiosa</em> 7
 19 -98.7
 20.15 2940 
 17 (AR54) <em>A.
 religiosa</em> 7
 20 -98.683
 19.083 3330 
 18 (AR55) <em>A.
 religiosa</em> 7
 20 -102.317
 19.383 3030 
 19 <em>A.
 religiosa</em> 7
 20 -99.267
 19.223 3369 
 20 <em>A.
 religiosa</em>  
 19 -98.055
 19.253 3358 
 21 <em>A.
 religiosa</em>  
 20 -103.642
 19.521 2928 
    
      
     
  
description: There are two files nuclear SSRs gene pop (.gen) for each
 species. micros_flinckii.gen (Nuclear SSRs
 for <em>Abies flinckii</em>)
 micros_religiosa.gen (Nuclear SSRs for <em>Abies
 religiosa</em>) Code: <em>A.
 flinckii</em> = <em>Abies flinckii</em>
 14 = <em>Abies flinckii</em>, population 1
 16 = <em>Abies flinckii</em>, population 2
 17 = <em>Abies flinckii</em>, population 3
 18 = <em>Abies flinckii</em>, population 4
 19 = <em>Abies flinckii</em>, population 5
 20 = <em>Abies flinckii</em>, population 6
 <em>A. religiosa</em> = <em>Abies
 religiosa</em> 12 = <em>Abies
 religiosa</em>, population 8 13 = <em>Abies
 religiosa</em>, population 9 15 = <em>Abies
 religiosa</em>, population 10 21 =
 <em>Abies religiosa</em>, population 11 22
 = <em>Abies religiosa</em>, population 12
 45 = <em>Abies religiosa</em>, population
 13 48 = <em>Abies religiosa</em>,
 population 14 49 = <em>Abies
 religiosa</em>, population 15 53 =
 <em>Abies religiosa</em>, population 16 54
 =<em> Abies religiosa</em>, population 17
 55 = <em>Abies religiosa</em>, population
 18 <em>Abies religiosa</em>, population
 19 AbM = <em>Abies religiosa</em>
 population 20 <em>Abies religiosa</em>,
 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.