Recent allopatric divergence and niche evolution in a widespread Palearctic bird,

the common rosench (Carpodacus erythrinus)

Chih-Ming Hung
a,b,c,
, Sergei V. Drovetski
d
, Robert M. Zink
a,b
a
Bell Museum, University of Minnesota, St. Paul, MN 55108, USA
b
Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
c
Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
d
Troms University Museum, NO-9037 Troms, Norway
a r t i c l e i n f o
Article history:
Received 3 December 2011
Revised 8 September 2012
Accepted 14 September 2012
Available online xxxx
Keywords:
Coalescence
Simulation
Species distribution model
Niche divergence
Phylogeography
a b s t r a c t
A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic
common rosench (Carpodacus erythrinus) suggested the existence of three recently diverged groups, cor-
responding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the
mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA
gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two
groups. However, UPGMA clustering of mtDNA U
ST
-values among populations recovered the three
groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent
divergence and insufcient time for sorting of alleles. Overall, coalescence methods indicated a lack of
gene ow among the three groups, and population expansion in the central-western and northeastern
Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity.
A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups,
which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of
ecological speciation. We showed that the early stages of speciation were not accompanied by ecological
niche divergence, consistent with other avian studies.
2012 Elsevier Inc. All rights reserved.
1. Introduction
Quaternary climatic uctuations repeatedly shifted the distri-
butions of species, presumably resulting in multiple cycles of
retraction into refugia during glacial advance and subsequent
expansion during interglacial periods (Hewitt, 2000, 2004). These
uctuations in range could have had at least three consequences:
(1) initiation of divergence among populations, (2) continued
maintenance of already distinct populations, or (3) merging of
once-differentiated populations. Phylogeographic studies can pro-
vide a description of the current geographic deployment of genetic
variation and yield inferences about which of these potential histo-
ries was experienced by a particular species (Avise, 2000). For
example, the discovery of three phylogroups in an extant species
implies the existence of at least three glacial refugia at the Last Gla-
cial Maximum (LGM; 21,000 years ago), assuming that the groups
evolved prior to the last glacial period. A species distribution model
(SDM), often referred to as an ecological niche model (Peterson
et al., 1999), can be used to determine the sizes and locations of
LGM refugia and then relate them to the current population struc-
ture (Carnaval et al., 2009; Knowles and Alvarado-Serrano, 2010).
One could also discover whether these intraspecic groups have
diverged ecologically, providing a test of the tenets of ecological
speciation (Schluter, 2009; McCormack et al., 2010). Peterson
et al. (1999) suggested that ecological divergence only occurred
after speciation; however, there are relatively few tests of niche
divergence early in the speciation process.
The common rosench (Carpodacus erythrinus) inhabits various
types of woodlands and grasslands, spanning much of the Palearc-
tic. During the past century, its range has expanded westward into
Scandinavia, France, Spain and England (Cramp and Perrins, 1994;
Payevsky, 2008), although persistent breeding is limited to Scandi-
navia. Pavlova et al. (2005) surveyed mtDNA variation and postu-
lated the existence of three taxa corresponding to the Caucasus
(CA), northeastern Eurasia (NEE), and central-western Eurasia
(CWE, Fig. 1). However, the geographic limits of the groups were
unclear and maximum likelihood estimates of migration suggested
a low level of gene ow among groups. In this study, we re-
examined the conclusion of Pavlova et al. (2005) by (1) using
robust coalescence methods and adding a Z-linked gene, (2) using
a SDM to reconstruct the current and LGM distributions of the
common rosench, to search for sites of potential refugia, and to
1055-7903/$ - see front matter 2012 Elsevier Inc. All rights reserved.
http://dx.doi.org/10.1016/j.ympev.2012.09.012

Corresponding author at: Department of Life Science, National Taiwan Normal

University, Taipei 116, Taiwan. Fax: +1 612 624 6777.
E-mail address: hungx037@umn.edu (C.-M. Hung).
Molecular Phylogenetics and Evolution xxx (2012) xxxxxx
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Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
assess the relative sizes of populations at each time, and (3) testing
for ecological divergence between these groups to determine if
niche differentiation has accompanied the early stages of lineage
divergence (Warren et al., 2008).
2. Methods and materials
2.1. Genetic analyses
We used the ND2 sequence data for 186 common rosenches
from Pavlova et al.s (2005) study (Fig. 1 and Table S1, NCBI acces-
sion numbers AY703261-AY703446). In addition, one Z-linked in-
tron, ADAMTS6 (Backstrm et al., 2006), was sequenced for 28
individuals from 15 localities (Table S1; 12, 7, and 9 individuals
from the three mtDNA-dened groups, CWE, NEE and CA, respec-
tively). Phases of sequences containing indels were sorted manually
by subtracting chromatogrampeaks upstreamof the indel in the re-
verse primer sequences from the double peaks downstream of the
indel in the forward primer sequences. This procedure was re-
peated in the alternative direction and allowed the two alleles of
a heterozygous individual to be determined (Sousa-Santos et al.,
2005; Dolman and Moritz, 2006). Alleles present in individuals with
multiple heterozygous sites but no indel(s) were resolved using
PHASE 2.1.1 (Stephens et al., 2001; Stephens and Scheet, 2005).
2.2. Detection of population division
NETWORK 4.5.1.6 (uxus-engineering.com) was used to gener-
ate minimum spanning networks (Polzin and Daneschmand, 2003)
for mtDNA and ADAMTS6 data to detect geographic partitioning of
haplotypes and alleles.
Pairwise U
ST
-values of mtDNA (but not ADAMTS6 due to small
sample sizes) among populations were estimated using DnaSP 5
(Librado and Rozas, 2009). To determine the overall geographic
pattern of population structure, we pooled individuals from each
locality and then clustered the matrix of pairwise U
ST
values using
the unweighted pair-group method using arithmetic averages (UP-
GMA) implemented in MEGA 4 (Tamura et al., 2007). We combined
the populations with sample sizes smaller than ve with samples
in the nearest and sufciently large population to avoid bias in
U
ST
estimates. If the combination was not geographically reason-
able, the samples were excluded from analyses. For example, the
Sakhalin population was not combined with the Kamchatka or
Magadan population because they are separated by a wide area
of sea or a long geographic distance.
We also applied spatial analysis of molecular variance imple-
mented in SAMOVA 1.0 (Dupanloup et al., 2002) to the mtDNA data
to explore population division. Based on an F-statistic, SAMOVA
uses a simulated annealing procedure to determine groups of pop-
ulations that are geographically and genetically homogeneous and
maximally differentiated from each other (i.e., the conguration
has the largest U
CT
). We tested population partitions (K) ranging
from 2 to 8 with 100 to 300 initial conditions each based on 10
5
annealing permutations. Given that populations with small sample
sizes might be erroneously identied as isolated groups in SAM-
OVA (Dupanloup, pers. comm.), we combined the localities with
small sample sizes according to the same rules we used for calcu-
lating the pairwise U
ST
-values.
2.3. Estimates of demographic parameters
A coalescence-based program, IMa (Hey and Nielsen, 2007), was
used to estimate the effective population sizes of two current pop-
ulations and their common ancestral populations (h
1
, h
2
, and h
a
;
h = 4 N
e
l), migration rates (m
1
and m
2
; m = m/l), and divergence
times (t = t l) between groups of populations determined from
the procedures outlined above. The UPGMA phenogram based on
pairwise U
ST
values and SAMOVA suggested two possible group
structures, a three-group model and a two-group model (see Sec-
tion 3.1). The three-group model included CA, CWE, and NEE. The
two-group model consisted of a combined CWE and NEE (termed
ME) and CA. We estimated the demographic parameters associated
with the various groupings in the two alternative models. We did
not use IMa2 (Hey, 2010) because we cannot specify a tree topology
for the three groups. A minimum of two independent analyses of
>2 10
7
steps after a burn-in of 10
6
steps were performed for each
pairwise comparison. Plots of trend lines and the effective sample
size values (ESS > 250) were examined to assess convergence in
parameter estimates. The IMa estimates were based on all available
mtDNA and ADAMTS6 sequence data combined. To convert the
scaled demographic parameters to absolute values, we calculated
the geometric mean of the substitution rates of ND2 and ADAMTS6
by multiplying the sequence lengths by 4 10
8
substitutions/site/
year for ND2 (Arbogast et al., 2006) and 1.62 10
9
substitutions/
site/year for ADAMTS6 (Ellegren, 2007; given the mean divergence
of Z-linked introns between chicken and turkey is 1.2 times higher
than that of autosomal introns, which have an average rate of
1.35 10
9
substitutions/site/year) and assumed a generation time
of 2 years (Stjernberg, 1979). The substitution rate used in this
study was higher than widely used rates for avian mtDNA (Lovette,
DOR
TV
TYV
GOR
IRK
KRY
YEK
MEZ
MED
MOS
KUR
KRD
SAK
KHA
MAG ANA
KAM
ALM
C. e. grebnitskii
C. e. erythrinus
C. e. kubanensis
C. e. ferghanensis
Fig. 1. Breeding range of the common rosench (Carpodacus erythrinus) with four subspecies indicated and location of sample sites (re-drawn from Fig. 1 in Pavlova et al.
(2005). Gray area indicates breeding range. Large solid circles indicate sample sizes of 10 or more individuals. Dotted lines partition the population into three groups as
indicated by the pairwise mtDNA U
ST
analysis (Pavlova et al., 2005) and the UPGMA tree based on a matrix of mtDNA U
ST
values (Fig. 4 in this study). ALM is Almaty, ANA is
Anadyr, DOR is Dornod, GOR is Gorno-Altay, IRK is Irkutsk, KAMis Kamchatka, KHA is Khabarovsk, KRD is Krasnodar, KRY is Krasnoyarsk, KUR is Kursk, MAG is Magadan, MED
is Medvedevo, MEZ Mezen, MOS is Moscow, SAK is Sakhalin, TV is Tv, TYV is Tyva, and YEK is Yekaterinburg.
2 C.-M. Hung et al. / Molecular Phylogenetics and Evolution xxx (2012) xxxxxx
Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
2004; Weir and Schluter, 2008) but more appropriate for recent
divergences (Ho et al., 2005; Arbogast et al., 2006; Herman and
Searle, 2011; but see Emerson 2006).
2.4. Group delimitation using hypothesis testing
We tested alternative population models using a coalescent
simulation program, SIMCOAL 2.1.2 (Laval and Excofer, 2004) to
simulate ND2 sequences. The simulations were performed using
the demographic parameters estimated from IMa based on mtDNA
and ADAMTS6, i.e., current effective population sizes (the effective
population size of mtDNA, N
ef
, was assumed to be half of the N
e
of
populations), migration rates, divergence times, exponential
growth rates (calculated from the current and ancestral population
sizes), a substitution rate of 4 10
8
substitutions/site/year, and
the generation time of two years.
One two-group model and two three-group models were simu-
lated (Fig. 2). In the latter case, two models were considered due to
the uncertainty in gene ow from NEE to CWE based on the IMa
analyses (see Section 3.1). One three-group model postulated no
gene ow (Fig. 2a) and the other assumed a low level of gene ow
(2 10
6
per generation per individual; see Section 3.1) from NEE
to CWE (Fig. 2b). Given that the dispersal distance of rosenches is
unlikely to span the entire geographic range, the widely distrib-
uted ME (in the two-group model; Fig. 2c) was not assumed to
be panmictic. We simulated ME by connecting two subgroups with
a substantial level of migration, 100 individuals per generation at
present but decreasing exponentially backwards in time as the
population size decreased (Fig. 2c). This level of migration is large
enough to prevent population differentiation (Hudson and Coyne,
2002). The ratio of N
e
for the two subgroups in ME was 12:1
(Fig. 2c) similar to that for CWE and NEE.
We simulated 5000 datasets of 186 ND2 sequences (1041 bp)
for each hypothesized model. The simulated datasets were ana-
lyzed using Arlequin 3.1 (Schneider et al., 2000) to calculate U
ST
values (Excofer et al., 1992) and the distribution and the upper
and lower bounds of 95% ranges of these values were recorded.
The U
ST
values for simulated data were compared with the empir-
ical U
ST
to evaluate which model was most consistent with the ob-
served data.
2.5. Species distribution modeling
Online databases ORNIS and GBFI together with our own mu-
seum data resulted in 196 breeding localities (see Fig. S1), which
we input into MAXENT v 3.2.2. (Phillips et al., 2006) to infer a
SDM. Because the species has only colonized western Europe dur-
ing the past few decades (Cramp and Perrins, 1994), we excluded
breeding records from Scandinavia, France, Spain and England.
We obtained climatic data (19 layers) for present and LGM condi-
tions from the Worldclim bioclimatic database (Hijmans et al.,
2005). We ran MAXENT ve times (using 30% of values for training)
and examined the jackknifed contributions of each bioclimatic
layer, picking seven layers (bioclim layers 1, 5, 9, 10, 11, 15 and
18) that contributed 5% or more to the total variation for the nal
analysis (Brown and Knowles, 2012). For the nal model, we con-
structed a SDM from the average of 10 MAXENT runs using all
locality points, which we displayed using DIVA-GIS ver. 7.1.7.2
(Hijmans et al., 2004).
2.6. Niche divergence tests
We used the program ENMTools v.1.3 (Warren et al., 2010) to
perform niche identity tests and background tests for whether taxa
that were dened according to the genetic data (i.e., the CA, CWE
and NEE groups) exhibit niche divergence or conservatism (or nei-
ther). The niche identity test assesses whether the similarity be-
tween ecological niches of two taxa is signicantly different from
a null distribution generated from random draws of pooled empir-
ical occurrence points. The identity test often suggests that two taxa
have signicantly different niches (Godsoe, 2010; Warren et al.,
2008). However, this inference is only true when the two groups
tolerate the exact same set of environmental conditions and have
the same suite of environmental conditions available to them
(Warren et al., 2010). Because this is unlikely for allopatric popula-
tions that are distributed across environmental gradients, the back-
ground test determines whether two taxa are more or less similar
than expected based on the differences in the environmental back-
ground where they occur. The background test determines whether
an empirical niche similarity index between two taxa is signi-
cantly smaller (niche divergence) or greater (niche conservatism)
than a null distribution of the niche similarity indices between
one taxon and random points from the environment within the
other taxons range; two null distributions result because the com-
parisons are done in both directions (Warren et al., 2010). For the
background tests, we divided the large central area of rosench dis-
tribution into eastern (CWEE) and western (CWEW) groups to ac-
count further for the large geographic distance involved.
3. Results
3.1. Population structure
The mtDNA network revealed that 9 of the 13 haplotypes from
the Caucasus (CA) formed a clade, which was separated by a few
steps from the remaining haplotypes (Fig. 3a). The haplotypes in
N
CA
=
83,000
N
CWE
=
3,516,000
N
NEE
=
308,000
N
a
= 63,000
t= 39,200
N
CA
=
72,000
N
ME
=
3,990,000 + 333,000
N
a
= 72,000
t =33,200
(a) (c) (b)
m= 2 10
-6
N
CA
=
83,000
N
CWE
=
3,516,000
N
NEE
=
308,000
N
a
= 63,000
t= 39,200
Fig. 2. Outline of two three-group models (a and b) and one two-group model (c) developed to test hypothesized demographic histories for the common rosench. N
a
, N
CA
,
N
CWE
, N
NEE
and N
ME
indicate effective population sizes of ancestral, CA, CWE, NEE and ME groups, respectively. t indicates time of divergence in units of generations from
present. Arrows indicate gene ow. The immigration rate (m) in the (b) model is shown in the gure. The dashed lines indicate that the groups are connected to each other
with substantial levels of gene ow.
C.-M. Hung et al. / Molecular Phylogenetics and Evolution xxx (2012) xxxxxx 3
Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
northeastern Eurasia (NEE) were not separated from those in cen-
tral-western Eurasia (CWE). Thus, the mtDNA network revealed
limited geographic structure. The allele network for ADAMTS6
showed no geographic structure (Fig. 3b). The UPGMA phenogram
based on the matrix of mtDNA pairwise U
ST
values (see Table S2
for the U
ST
values) clustered rosench populations into three dis-
tinct groups corresponding to CA, NEE, and CWE groups (Fig. 4).
The SAMOVA supported a two-group structure, CA and all remain-
ing populations (i.e., CWE plus NEE). The U
CT
value was highest
when K = 2 (U
CT
= 0.349) and decreased as K increased.
IMa analyses based on mtDNA, and mtDNA plus ADAMTS6, sug-
gested recent isolation with little or no gene ow followed by pop-
ulation expansion (except for CA), for both the three-group and
two-group models. In addition, the IMa analyses revealed that the
values of demographic parameters for the two datasets differed in
magnitude, with the combined data (i.e., mtDNA plus ADAMTS6)
suggesting longer divergence times, greater effective population
sizes and lower migration rates (Table S3). We used results based
on the combined dataset in our simulations. For the three-group
model, IMa revealed that the current population sizes of CWE
(7,032,000; 95% credibility interval [CI] = 4,130,000 to 17,303,000)
and NEE (616,000; 95% CI = 334,0001,839,000) are signicantly
larger than that of the ancestral population (136,000; 95%
CI = 58,000240,000), whereas the current population size of CA
(167,000; 95% CI = 80,000438,000) was not signicantly larger
than that of the ancestral population (Fig. 5a and b). There was little
if any migration between any pair of groups (Fig. 5ce). There could
Fig. 3. Network of (a) mtDNA and (b) a Z-linked intron (ADAMTS6) haplotypes of the common rosench by the minimum spaning criterion. Colors on the network indicate
the locations at which each haplotype was detected. Black circles indicate central-western Eurasian (CWE) haplotypes, white circles indicate northeastern Eurasian (NEE)
ones, and gray circles indicate Caucasian (CA) ones. Open triangles indicate unsampled or extinct haplotypes. Sizes of circles are proportional to haplotype frequencies. Short
lines indicate one mutation step.
Fig. 4. UPGMA phenogram showing relationships among rosench population
samples. The tree is reconstructed based on the matrix of U
ST
values. The three
clades correspond to the central-western Eurasian (CWE), northeastern Eurasian
(NEE), and Caucasian (CA) groups. Populations with sample sizes smaller than ve
were combined with samples in the nearest and sufciently large population.
Therefore, DOR + TV is the combination of Dornod and Tvs samples, IRK + KRY is
that of Irkutsk and Krasnoyarsk, MED + MEZ is that of Medvedevo and Mezen, and
MOS + KUR is that of Moscow and Kursk.
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Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
be some migration from NEE to CWE (2 10
6
per generation per
individual; 95% CI = 0 to 1.6 10
5
[we could not reject the pos-
sibility of zero gene ow]; Fig. 5d). The divergence times between
CA and CWE (78,300 years ago; 95% CI = 52,200117,000 years
ago), between CWE and NEE (78,800 years ago; 95% CI = 52,000
117,200 years ago), and between CA and NEE (76,200 years ago;
95% CI = 42,200141,700 years ago) were similar and recent
(Fig. 5f), suggesting contemporaneous origins of the three groups
(see Hung et al. 2012). The IMa results for the two-group model re-
vealed that the current population size of ME (8,645,000; 95%
CI = 5,396,00018,196,000) was signicantly larger than the ances-
tral population (147,000; 95% CI = 88,000282,000), but that of CA
(144,000; 95% CI = 70,000394,000) was not. The IMa results
showed no migration between the two groups. The estimated
divergence time (66,400 years ago; 95% CI = 45,50096,600 years
ago) was similar to that of the three-group model.
Comparison of the simulated and empirical data supported the
three-group models over the two-group model (Fig. 6). The empir-
ical U
ST
value was within the 95% distribution range of U
ST
values
of the three-group models regardless of the level of gene ow
(Fig. 6a and b) but out of the 95% range of U
ST
values for the
two-group (Fig. 6c). Therefore, we could reject the two-group but
not either of the three-group models. The similarity between the
distributions of U
ST
values for the two three-group models, one
with and one without gene ow, suggested that the level of gene
ow from NEE to CWE was negligible.
3.2. Current and LGM distributions predicted by SDM
The AUC of the MAXENT distribution model was 0.88, indicating
good quality in the predictions (AUC > 0.7 = informative; Baldwin,
2009; Swets, 1988). The SDM under current climatic conditions
predicted the breeding range of common rosenches including
newly colonized areas in Scandinavia (Fig. 7a). Although the model
predicts occurrence in France, Portugal and Spain the species has
not yet become established in these areas, but there are sporadic
records (Cramp and Perrins, 1994). Therefore, the predicted cur-
rent distribution of common rosenches in Europe was somewhat
wider than the observed distribution but consistent with the trend
Fig. 5. The marginal posterior probabilty distribution of the IMa parameters under the three-group model. The three groups are Caucasus (CA), central-western Eurasia (CWE)
and northeastern Eurasia (NEE). The IMa analyses were based on mtNDA and a Z-linked gene (ADMATS6) combined. Effective population sizes, h, for CA, CWE, NEE and their
ancestral populations are shown in (a and b). Migration rates, m, in two directions between CA and CWE, between CWE and NEE, and between CA and NEE in the unite of per
generation per individual are shown in (ce). Divergence times, t, for the three pairwise comparisons in the unite of year are shown in (f).
C.-M. Hung et al. / Molecular Phylogenetics and Evolution xxx (2012) xxxxxx 5
Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
of recent expansion towards the western and northwestern Pale-
arctic (Cramp and Perrins, 1994; Payevsky, 2008).
The predicted distribution at the LGM suggested that common
rosenches mainly occurred in four areas (i.e., refugia): (1) Kam-
chatka and Magadan, (2) southern Siberia, Mongolia, China and Ja-
pan, (3) Caucasus and (4) southern Europe (Fig. 7b). The rst three
predicted refugia sustainably or partially overlapped with the pres-
ent distributions of the three haplotype groups. Comparing the ex-
tent of the present and LGM distributions suggested that the
Caucasian population (CA) and Kamchatka and Magadan popula-
tions (corresponding to NEE) had not undergone expansion
whereas the other populations (corresponding to CWE) expanded
westwards since the LGM (Fig. 7).
3.3. Niche divergence
The pairwise niche identity tests (not shown) suggested that the
niches of different groups of rosenches were signicantly differ-
ent based on the niche similarity index, Schoeners D (P < 0.001).
However, we found no instances of either niche divergence or
niche conservatism in the eight pairwise background tests, which
took into account the environment available to each group (Fig. 8).
4. Discussion
Our re-analyses of the mtDNA data, and analyses of the mtDNA
data plus the sex-linked sequences, support the existence of three
groups of populations in the common rosench, namely the Cauca-
sus, northeastern Eurasia, and central-western Eurasia. These three
groups are not reciprocally monophyletic for either mtDNA or the
Z-linked gene tree, suggesting that the rosenches are at an early
stage of diversication. Our estimates of gene ow were essentially
zero, indicating that the groups are evolving independently. Hence
we infer that speciation has commenced. In addition, the SDM im-
plies that these three groups might have occupied distinct LGM
refugia. Further supporting our hypothesis of the distinctness of
these groups, we note that the three groups, CA, NEE and CWE, cor-
respond to named subspecies, C. e. kubanensis, C. e. grebnitskii and
C. e. erythrinus, respectively (Cramp and Perrins, 1994; Fig. 1). The
subspecies C. e. kubanenesis is larger and more rosy-red colored
Fig. 6. Histograms of U
ST
values for 5000 simulated sequence datasets. (a) Results from simulations of the three-group model without gene ow. (b) Results from simulation
of the three-group model with a low level of gene ow from NEE to CWE. (c) Results from simulations of the two-group model. The dashed lines represent the 2.5 and 97.5
percentiles in the distribution. The black triangles represent the U
ST
value of our empirical data.
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Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
than the nominate subspecies C. e. erythrinus, and C. e. grebnitskii
has more red or carmine on its upperparts than C. e. erythrinus
(Clement et al., 1993; Cramp and Perrins, 1994). A fourth subspe-
cies, C. e. ferghanensis, represented only by our Almaty sample
was not genetically distinct, and fell within C. e. erythrinus.
Although we do not propose elevating these taxa to species, any
analysis of recent trends in biodiversity should recognize their his-
torical existence.
4.1. Recent history of common rosenches revealed by phylogeography
and SDM
The application of SDMs to evolutionary studies is promising
(Carnaval et al., 2009; Kozak et al., 2008) although their perfor-
mance has been under debate (e.g., Arajo et al., 2009; Beale
et al., 2008). Our SDM under current climatic condition predicted
the occurrence of common rosenches in western Europe even
though our model did not incorporate breeding sites from this re-
gion. The fact that the species has recently become common in
Scandinavia and has bred locally in other European areas (Cramp
and Perrins, 1994; Payevsky, 2008), and that the considerable part
of the predicted range conforms to the known distribution, sug-
gests that our SDM is relatively robust. However, our SDM under-
estimated the distribution of this species in northeastern Eurasia
and overestimated that in China and Japan when compared with
the known distribution. The inconsistency may reect limitations
of SDMs and/or the fact that our knowledge about the distribution
of this species in these regions is incomplete.
In general, it is difcult to determine the specic geographic
locations of LGM refugia, irrespective of whether one uses a SDM
or makes inferences from the extant phylogeographic pattern.
We consider our SDM and genetic results to be reciprocally illumi-
nating. Our SDM (Fig. 7) is a snapshot at the maximum of the last
glacial period, which began ca. 100,000 years before (Lisiecki and
Raymo, 2007), and hence it is unclear how many refugia existed
during this period. Our genetic results suggested three recently
(e.g., ca. 75,000 ybp) isolated groups (Figs. 4 and 6), which we think
helps guide interpretation of the SDM. Assuming that the three
groups originated prior to the LGM, we suggest that two refugia ex-
isted in the eastern Palearctic at the LGM, even though our SDM
shows a relatively narrow gap (i.e., the coast near the northwestern
tip of the Sea of Okhotsk) between them (Fig. 7b). However, many
extant phylogroups are parapatrically distributed or separated by
narrow gaps (e.g., Hung et al., 2012; Zink et al., 2008). The lack
of sorting of mtDNA haplotypes from the Palearctic (excluding
CA; Fig. 3a) coupled with the inference of negligible gene ow be-
tween NEE and CWE, is consistent with our estimate of divergence
time (ca. 75,000 ybp). Haploid, non-recombining mtDNA gene
trees require isolation lasting approximately N
e
generations to
reach reciprocal monophyly (Hudson and Coyne 2002). Given the
large estimates of N
e
for the two main Palearctic groups
(7,032,000 and 616,000), considerable time would have to
elapse before the mtDNA gene tree would become reciprocally
Fig. 7. Predicted distributions of the common rosench (Carpodacus erythrinus) for (a) present and (b) LGM. Darker colors reect areas with higher probabilities of occurrence.
C.-M. Hung et al. / Molecular Phylogenetics and Evolution xxx (2012) xxxxxx 7
Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
monophyletic. Therefore, there has been insufcient time for the
mtDNA gene tree to evolve to reciprocal monophyly. Given that
the average N
e
of Z-linked genes is three times greater than mtDNA,
we expected that the ADSMTS6 gene tree would show less geo-
graphic structure than the mtDNA gene tree, which we observed.
Combining coalescence and SDM analyses allowed additional
insight into rosench population history. Our coalescence analyses
revealed that CWE and NEE experienced population expansion,
whereas CA did not (Fig. 5). Our SDM analyses suggested a similar
history except that NEE had similar distributions between the
present and LGM predictions. However, the degree of expansion
for CWE was at least 10 times greater than that for NEE according
to the coalescence analyses (Fig. 5), and from the SDM it would ap-
pear logical given the large area into which CWE expanded, and the
relatively stable distribution of NEE.
The predicted LGM occurrence of rosenches in areas south of
where they presently occur in southern Europe is relevant to past
hypotheses about the distribution of genetic variation following
glacial retreat. Hewitt (2004) suggested that genetic variability de-
creases in the direction of colonization from a refugium owing to
sampling effects, termed leading edge expansion. However, if
the refugium no longer has suitable habitat, as is the case for com-
mon rosenches in southern Europe, this prediction is not testable.
In this case, one might look to the southern extent of the current
range as being the closest to refugial populations, and hence cur-
rently harboring the greatest genetic variability, but we lacked
data for a strong test of this hypothesis. Thus, a SDM can modify
predictions about post-glacial patterns of genetic variation.
The SDM is consistent with a history of isolation for rosench-
es in the Caucasus (Fig. 7). Compared to CWE and NEE, CA has a
relatively smaller effective population size and has not experi-
enced population expansion. These attributes can explain why
approximately 70% of haplotypes in CA form a clade in the
mtDNA tree (Pavlova et al. 2005) and haplotype network
(Fig. 3), whereas haplotypes in the other two groups do not. That
is, lineage sorting is a function of Ne, and therefore one expects
faster sorting in the CA group. We predict that if the isolation
and current population size continues, the Caucasian population
will be the rst group to become a new species. This example
illustrates that relatively small and isolated populations on is-
lands, continental habitat islands, or mountaintops are potent
grounds for lineage diversication.
4.2. Niche evolution between the recently diverged common rosench
groups
As the three rosench groups are in the early stages of specia-
tion, our study can help to show whether ecological divergence
drives speciation or accrues after speciation. We found no evidence
for niche divergence, a result consistent with that for other groups
of birds that are considerably more differentiated (Peterson et al.,
1999; McCormack et al., 2010). The signicant tests for niche iden-
tity coupled with the insignicant background tests reinforce the
importance of considering environment availability when testing
niche divergence (McCormack et al., 2010). In other words, the re-
sults imply that rosenches in different areas do not have the same
niche space available to them.
The lack of support for niche divergence or conservatism may
indicate that rosenches can survive in varied habitats, as sug-
gested by the signicant niche identity tests. This may explain
the recent population expansion of rosenches shown by genetic
data and current expansion to new ranges in Europe. On the other
hand, given the general lack of niche divergence, one might expect
that the groups would invade each others ranges. That is, during
Fig. 8. Background tests for niche divergence. Arrows indicate observed niche similarity index (Schoeners D) between two groups and are compared with a null distribution
for the niche similarity indices between one group and random points from the range of the other group and vice versa. (a) Gray histogram indicates a null distribution of NEE
versus the background of CWEE, and black indicates the opposite comparison. (b) Gray indicates a null distribution of CA versus the background of NEE, and black indicates
the opposite comparison. (c) Gray indicates a null distribution of CA versus the background of CWEW, and black indicates the opposite comparison. (d) Gray indicates a null
distribution of CWEW versus the background of CWEE, and black indicates the opposite comparison. Niche similarity values smaller than a null distribution indicate niche
divergence, larger values indicate niche conservatism, and values within a null distribution indicate neither niche divergence nor niche conservatism.
8 C.-M. Hung et al. / Molecular Phylogenetics and Evolution xxx (2012) xxxxxx
Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012
the ensuing 21,000 years since the LGM, and a dispersal distance
typical for passerine birds of P1 km per generation (Barrowclough
1980), there would have been ample time for range expansion and
homogenization of the three groups. However, our estimates of
gene ow suggest this is not occurring. Hence it is possible that
the forms exclude each other behaviorally (Waters, 2011) or we
have not captured the most important niche dimensions.
Acknowledgments
We thank S. Rohwer for his roles in gathering specimens and A.
Pavlova for doing the original analyses, and S. Birk for loans.
K. Kozak and D. Shepard helped in conducting ecological niche
modeling. T. Rodrigues assisted with map making. B. McKay, H.
Vazquez and two anonymous reviewers helped to improve the
manuscript. We are grateful to the University of Minnesota Super-
computing Institute for assistance with the computations. Support
came from NSF (DEB 9707496, and DEB 0212832), FCT (PTDC/BIA-
BEC/103435/2008) and the Dayton-Wilkie fund of the Bell Museum.
Supplementary material
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.ympev.2012.09.
012.
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Please cite this article in press as: Hung, C.-M., et al. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rose-
nch (Carpodacus erythrinus). Mol. Phylogenet. Evol. (2012), http://dx.doi.org/10.1016/j.ympev.2012.09.012