Population genetics and metapopulation

dynamics of the species

Spergularia echinosperma

Pavel Kúr
Supervisor: Milan Štech
Isoëto-Nano-Juncetea
> vegetation of annual wetland herbs
Introduction
> exposed bottoms of periodically flooded artificial ponds or natural lakes
> habitat for many endangered species of Europe
> metapopulation dynamics to some extent affected by the fragmentary character
of the biotope
> poorly studied ecological group (cf aquatic plants)
Aquatic plants Hygrophilous plants
(Lemnetea, Potametea) (Isoëto-Nano-Juncetea)
Life history perennials, clonal growth, annuals, short life cycle, persistent seed bank
vegetative spread
hydrochory, well-documented hydrochory probably limited, long-distance seed
Dispersal long-distance dispersal with dispersal poorly documented, possible role of
waterfowl fish transport

Model species: Spergularia echinosperma

(Caryophyllaceae)
> exclusively restricted to exposed pond
bottoms and oxbow lakes
> strongly endangered
> endemic to Central Europe: Czechia +
Germany (+Slovakia, ?Austria, ?Poland)
> diploid (2n = 2x = 18)
Questions asked
1) What is the distribution of genetic variation within and among populations of S. echinosperma?
2) Which model describes best the species migration?
> On which geographical scale does isolation by distance play a role?
> Which factors affect the amount of gene flow between the species populations (drainage divides, fish companies)?
> What are the barriers for the species migration?
3) Which dispersal vectors can the species distribution be attributed to?
> hydrochory × zoochory × anthropochory
 Methods
Sampling sites
• 23 populations from Czech Republic and Germany
• (1-)5-10 plants / population, 186 individuals total
• mainly fish ponds and fish storage ponds (+ 2
oxbow lakes in Germany, 1 reservoir in E Moravia)
• classified into 9 groups based on river catchments
and geomorphological criteria

Cladogram based on population along-stream distances

(Ward clustering)
Region Watershed
Svihov  Železné hory Mts.
Schonberg
Werder
Elbe Region
Vosecky Javořice Highlands
Hrachoviste
Tobolky
Sluzebny Třeboň Basin
Stolec
Hodemysl
Breznice Highlands
Podhursky Elbe
Driten
Mlynhor České Budějovice Basin
Skopec
Cky
Hurka
Chvalovec
Jensov Blatná Highlands
Malobor
Stasov
Nohavice
Kojatin Křižanov Highlands Donau
Parezny
Terlicko Silesian-Moravian Foothills Oder
Methods Locus Motif
Allele
count
Ho He FIS
Population
# of
individuals
# of multi
locus Ho He FIS
SE1 GT 3 0.04 0.06 0.91 genotypes
Genetic analyses SE4 GTT 5 0.00 0.09 0.89 Cky 1 1 0.00 0.00 n.d.
> SSR SE8 CT 4 0.00 0.06 1.00
Driten 5 1 0.00 0.00 1.00
SE37 AC 2 0.04 0.04 1.00
> markers designed specifically for S. echinosperma SE69 CA 2 0.00 0.02 1.00 Hodemysl 10 3 0.00 0.04 1.00
> total of 16 loci used SE82 CA 3 0.00 0.03 0.91
Hrachoviste 10 2 0.00 0.02 1.00
SE91 CAA 4 0.00 0.05 1.00
SE108 TTG 5 0.01 0.07 0.91 Hurka 7 2 0.00 0.02 1.00
SE151 CA 2 0.00 0.03 1.00 Chvalovec 10 2 0.00 0.03 1.00
SE255 TTG 3 0.00 0.03 1.00
SE261 CAA 2 0.00 0.03 1.00 Jensov 10 3 0.01 0.04 0.98
SE451 AC 2 0.04 0.02 1.00 Kojatin 8 1 0.00 0.00 1.00
SE495 TTG 3 0.00 0.01 1.00 Malobor 10 2 0.01 0.01 0.94
SE548 GTT 2 0.00 0.00 1.00
SE677 TGT 6 0.00 0.05 0.91 Mlynhor 10 5 0.00 0.12 1.00
SE906 CAA 2 0.04 0.02 1.00 Nohavice 10 3 0.00 0.29 1.00

Ho – observed heterozygosity Parezny 10 4 0.01 0.06 0.94

He – expected heterozygosity Podhursky 10 1 0.00 0.00 1.00
 34 unique multi locus genotypes in total FIS – averaged inbreeding coefficient
Schonberg 8 2 0.00 0.03 1.00
 nearly all homozygotes Skopec 7 2 0.00 0.02 1.00
 extremely high values of FIS Sluzebny 3 2 0.00 0.03 1.00
Stasov 10 2 0.00 0.02 1.00
Stolec 2 1 0.19 0.13 0.63
Svihov 8 1 0.00 0.00 1.00
Terlicko 10 2 0.00 0.01 1.00
Tobolky 9 2 0.00 0.01 1.00
Vosecky 9 2 0.00 0.01 1.00
Werder 9 2 0.06 0.08 0.88
South-West Bohemia
Between-individual genetic distances Results
Breznice Highlands (Podbrdsko)
> Microsatellite Analyzer (MSA) 4.05
Elbe
> delta-mu squared ([δμ]2) distances
+ Moravia (part)
Moravia + Silesia Železné hory Mts

S v ih o 0 0 1
Nohav008
Nohav009
Elbe Region
+ Javořice Highlands Javořice Highlands
Třeboň Basin
different symbol shapes = different populations Breznice Highlands
České Budějovice Basin
Blatná Highlands
1.5

Křižanov Highlands
Silesian-Moravian Foothills
PCoA Axis 2

Werde007
Werde006
Werde005
Werde008
Werde002 Ch
hval008
val005
Staso007 C
Chval006
Jenso007
Staso003 Sluze003
Skope005
Skope001

PCoA, computed in Canoco 5

-1.0

M ly n h 0 0 1
H u rk a 0 0 5
JMelyn ns oh 00 00 92
H u rk a 0 0 2
the 2 axes explain 95% of variation
Neighbor-joining
-1.5 PCoA Axis 1 2.0 computed in R, package ape
 Multi-locus genotypes
Results
Population differentiation
Bayesian clustering
> BAPS 6.0
> population mixture analysis, clustering of
individuals (no admixture revealed)
> best K = 9 (probability = 0.99)

Pairwise RST values

> Arlequin 3.5.1.2

> clear differentiation between Bohemia and

Bohemian-Moravian Highlands
> no differnetiation within the groups
> genetic relatedness of German populations
with some Moravian ones

Rst values
<0.00; 0.25>
(0.25; 0.50> different colors = BAPS groups
 AMOVA (Arlequin 3.5.1.2, RST-like differences, 1023 permutations)
Results
Sum of Variance Percentage Sum of Variance Percentage
Source of variation d.f. p d.f. p
squares components of variation squares components of variation
Regions Fish companies
Among groups 8 5102 13.6 68.1 <0.001 9 5304 14.4 71.3 <0.001
Among populations within groups 14 1129 5.1 25.8 <0.001 13 927 4.5 22.7 <0.001
Among individuals within populations 163 357 1.0 4.9 <0.001 163 357 1.0 4.9 <0.001
Within individuals 186 37 0.2 1.0 <0.001 186 37 0.2 1.0 <0.001
Total 371 6627 20.0 371 6627 20.0

Mantel tests (R 3.0.2, package ecodist, Spearman correlations, 1000 permutations)

Region matrix 1 matrix 2 matrix 3 r p
All populations geographical distances 0.56 0.001
> highest portion of genetic variation allocated
same fish companies* 0.30 0.002
among regions
same fish companies* geographical distances 0.04 0.560 > positive isolation-by-distance relation only
genetic distances ([δμ]2)
along-stream distances
0.62 0.001
thanks to the distances between the two
(Elbe watershed)
main genetic clusters
geographical distances
(Elbe watershed) 0.62 0.001 > no difference between direct distances and
South-West Bohemia geographical distances 0.18 0.158 along-stream distances
genetic distances ([δμ]2) along-stream distances 0.16 0.222 > fish companies do not contribute to
same fish companies* -0.05 0.610 population differentiation
B.-M. Highlands + genetic distances ([δμ]2) geographical distances 0.32 0.062
Silesia + Germany

* 0/1 matrix of whether a certain locality pair is controlled by the same fish company
 1 Spatial autocorrelation
All populations
(SPAGeDi 1.4, direct geographical distances, standard errors computed using
999 permutations)
Moran's I

Mean ± 2SE

-1
5

100
200
500
10
20
30
40
50

1000
0.1

Distance intervals [km]

2 1
South-West Bohemia B.-M. Highlands + Silesia
+ Germany
1
Morans's I
Moran's I

-1
-1
50

100

300

1000
0.1
5

10

20

50

100
0.1

Distance intervals [km] Distance intervals [km]

 Results
Morphological differentiation > seed color probably genetically conditioned
> two different morphotypes of S. echinosperma -> black-seeded type > supports classification of the types as separate
-> brown-seeded type taxa
> black-seeded type known from Bohemia > black-seeded type possibly endemic to Bohemia
> brown-seeded type widespread in Germany > brown-seeded type occurring in Germany from
> correlation between seed color and genetic clusters: where it extends to Moravia -> possible admixture
> revisions of herbarium specimens will reveal more

1.5
Bohemian-Moravian Highlands
1.5

Seed color:
+ Silesia + Germany black
brown
NA

PCoA Axis 2
PCoA Axis 2

-1.0
-1.0

South-West Bohemia

-1.5 PCoA Axis 1 2.0 -1.5 PCoA Axis 1 2.0

 Distribution of the association Polygono-Eleocharitetum ovatae Moravia-Germany connection
Hypotheses about long-
Localities of S. echinosperma + S. kurkae according to:  Florabase.cz > run-off of brown-seeded plants
range to Elbe
connections
 Slavík: Fytogeografické syntézy ! why no black-seeded plants in Gemany?
between populations
× long-range dispersal
? Moravia-Silesia connection
> S. echinosperma may be widespread in Silesian
lon
g-
ra
ng
ed
? Lowland (along Oder), just unreported
× long-range dispersal
isp
er
sa

?
l

×
ispersal
long-range d
 Summary

> two distinct genetic groups within S. echinosperma:

> South-West Bohemia
> Bohemian-Moravian Highlands + Silesia + Germany
> the genetic groups also morphologically differentiated – seed color
> isolation by distance works on large geographic scale only to some extent
> recent connections between Moravian and German and Moravian and Silesian populations
> either result of poorly documented species distribution or long-range dispersal
> (nearly) no genetic isolation by distance on small geographic scale
> bird migration or human activity (fish exchange between fish companies)