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Molecular Ecology Editorial 2012 and Referees 2011

Authors:
Editorial 2012
State of the journal
We are pleased to report that the state of the journal con-
tinues to be strong. Molecular Ecology’s impact factor as
calculated by ISI Web of Knowledge rose for the sixth
year in a row, from 4.301 in 2005 to 6.457 in 2010. The
journal currently ranks fifth in impact in both the
Ecology (130 journals) and Evolutionary Biology (45
journals) categories tracked by ISI. When only journals
publishing primary research articles are considered,
Molecular Ecology ranks second and third among Ecology
and Evolutionary Biology journals, respectively. The 414
articles published in Molecular Ecology in 2010 make it
one of the largest journals in ecology and evolutionary
biology as well, ranking third in both subject categories.
Announcements
Molecular Ecology Prize
The 2011 Molecular Ecology Prize was awarded to
Professor Deborah Charlesworth of the University of
Edinburgh for her pioneering studies of mating systems
and the origin of sex chromosomes. A biography of
Deborah and her contributions to molecular ecology
can be found on page 23 of this issue.
Molecular Ecology Symposium
In 2012 the first Joint Congress on Evolutionary Biology
(Evolution 2012) will be held in Ottawa, Canada’s capi-
tal city. This signal event will bring together five of the
world’s largest academic societies devoted to the study
of ecology and evolutionary biology: the American
Society of Naturalists (ASN), the Canadian Society for
Ecology and Evolution (CSEE), the European Society for
Evolutionary Biology (ESEB), the Society for the Study
of Evolution (SSE) and the Society of Systematic Biolo-
gists (SSB).
2012 also marks the 20th anniversary for Molecular
Ecology. To celebrate the tremendous advances that
have been made in this research area, as well as to
brainstorm about the future of the field, the journal is
sponsoring a Molecular Ecology Symposium on 6th July
2012 in Ottawa, the day before Evolution 2012 gets
underway. The structure of the meeting will follow the
basic format of Molecular Ecology, with plenary talks in
each of the journal subject areas, followed by panel dis-
cussions that will focus on future advances. To broaden
participation, the symposium will include an online
component, which will involve live streaming of the
talks and discussions involving both in-the-room dele-
gates and those participating online. The current speaker
line-up is available at http://www.molecularecologist.
com/ottawa-2012/.
Meta-analyses studies
With the widespread implementation of the Joint Data
Archiving Policy, large numbers of ecological and evo-
lutionary data sets are becoming available. Data archiv-
ing, combined with the enormous rate at which new
data are being generated, will allow us to address many
questions in ecology and evolution with a degree of
rigour and decisiveness that was not possible even
several years ago. Thus, we strongly encourage the sub-
mission of meta-analysis studies to Molecular Ecology.
Meta-analysis studies will typically be published as part
of our ‘Invited Reviews’ section, which will be renamed
‘Invited Reviews and Meta-analyses’. Louis Bernatchez
edits this section, and if you have a review or meta-
analysis study that you would like to develop for Molec-
ular Ecology please contact him (louis.bernatchez@bio.
ulaval.ca) to ensure that it is an appropriate topic for
the journal.
Data archiving
We have been delighted by the positive response to the
implementation of our Joint Data Archiving Policy at
the beginning of 2011. Following discussions with our
editors and authors, it is clear that the utility of
archived data is greatly enhanced when the scripts used
in the analyses are also made available. Given that
these scripts may be a mix of proprietary and freely
available code, we have decided against making their
deposition compulsory, but we nonetheless strongly
encourage authors to make these scripts available
whenever possible.
Reviewers
We wish to express our gratitude to our many referees
for the donation of their time to the journal and to the
2011 Blackwell Publishing Ltd
Molecular Ecology (2012) 21, 1–22 doi: 10.1111/j.1365-294x.2011.05381.x
discipline of molecular ecology; people who reviewed
for us between 1 November 2010 and 15 October 2011
are listed at the end of this editorial.
Editorial issues
Current standards for publication in Molecular
Ecology
One of the most challenging aspects of editing a large
journal like Molecular Ecology is maintaining consistency
in our editorial decisions across the wide range of top-
ics covered by the journal and among our highly
respected but diverse subject editors. This is exacer-
bated by the rapidly changing norms in the field in
terms of molecular tools and analytical approaches.
An especially contentious issue concerns the publica-
tion of phylogeographic studies based on the analyses
of a single locus. We sometimes choose not to review
such studies because conclusions drawn from such lim-
ited data may not be reliable. However, we do not have
a blanket policy to reject them without review because
there are questions for which analysis of a single locus
is appropriate. Authors, referees and editors have on
occasion suggested that we establish guidelines regard-
ing the minimum number of loci, populations and indi-
viduals for a study to be considered for publication in
Molecular Ecology. However, we have been reluctant to
formulate such guidelines because they would depend
on the question being addressed, the kind of molecular
markers employed, the geographic range of the focal
taxa and so forth. Likewise, such guidelines would have
to be modified on a yearly basis as standards of the
field continue to ratchet upwards. Nonetheless, we feel
that knowledge of current norms in Molecular Ecology
with respect to these parameters would be useful to our
authors and editors. Here we present information on
the numbers of loci, populations and individuals
employed by studies published in the journal from Jan-
uary to September 2011 (Figs 1 to 6; Tables 1–4).
There are no real surprises. For example, an average
of 17.4 microsatellite loci are employed in studies pub-
lished in the journal in 2011 (Fig. 1; Table 1). The larg-
est numbers of loci were assayed in studies of
‘Ecological Genomics’ and ‘Molecular Adaptation’ and
the fewest in studies of ‘Kinship, Parentage and Behav-
iour’ (Fig. 1). This difference is reasonable given that
many questions in the latter category can be answered
with 6–10 loci, whereas there is almost no limit to the
number of loci that can be useful in genome-wide scans
for evidence of selection.
Approximately half of microsatellite studies in the
subject categories ‘Phylogeography’ and ‘Speciation and
Hybridization’ also include information on organellar
variation. However, the inclusion of organellar data
was less frequent in other subject areas and absent in
studies of ‘Kinship, Parentage and Behaviour’ (Table 1).
5
10
15
20
25
30
35
40
150
200
250
300
Ecological genomics
Ecological interactions
Kinship, parentage and behaviour
Molecular adaptation
Phylogeography
Population and conservation genetics
Speciation and hybridization
Microsatellites
Fig. 1 Average number of microsatellite loci employed by
studies published in Molecular Ecology from January to
September 2011. Error bars indicate one standard deviation of
uncertainty.
100
200
300
400
500
600
700
800
10 000
15 000
20 000
25 000
30 000
35 000
40 000
Ecological genomics
Ecological interactions
Kinship, parentage and behaviour
Molecular adaptation
Phylogeography
Population and conservation genetics
Speciation and hybridization
SNPs
Fig. 2 Average number of single nucleotide polymorphisms
(SNPs) employed by studies published in Molecular Ecology
from January to September 2011. Error bars indicate one stan-
dard deviation of uncertainty.
2EDITORIAL AND RETROSPECTIVE
2011 Blackwell Publishing Ltd
The number of studies that employ single nucleotide
polymorphisms (SNPs) for inference about pattern and
process in molecular ecology is too small to make
meaningful comparisons between subject areas (Fig. 2;
Table 2). Nonetheless, it is clear that the number of
SNPs employed is typically more than 10 times that of
microsatellites. This is not surprising given that SNPs
are more amenable to high throughput genotyping than
microsatellites. Because the information content of
SNPs, which are bi-allelic, is much less than that of
microsatellites, it is reassuring that the reduced infor-
mation content per SNP is more than made up for by
the greater number SNPs that are assayed in an average
study when compared to microsatellites. Interestingly,
unlike microsatellite studies, articles that reported on
SNP variation rarely included organellar data.
Studies that employ nuclear genes for inference assay
fewer loci than do comparable studies with microsatel-
lite or SNP markers, although there are outlier studies
(Fig. 3; Table 3). This is especially true for ‘Phylogeog-
raphy’ studies or studies of ‘Ecological Interactions’
(Fig. 3). The relatively few nuclear genes assayed in
many studies presumably reflect the time and expense
associated with gathering sequence data for low-copy
Fig. 4 Average number of amplified fragment length polymor-
phisms (AFLPs) employed by studies published in Molecular
Ecology from January to September 2011. Error bars indicate
one standard deviation of uncertainty.
Fig. 3 Average number of nuclear genes employed by studies
published in Molecular Ecology from January to September
2011. Error bars indicate one standard deviation of uncertainty.
Fig. 5 Average number of populations analysed by studies
published in Molecular Ecology from January to September
2011. Error bars indicate one standard deviation of uncertainty.
Fig. 6 Average number of individuals analysed by studies
published in Molecular Ecology from January to September
2011. Error bars indicate one standard deviation of uncertainty.
EDITORIAL AND RETROSPECTIVE 3
2011 Blackwell Publishing Ltd
Table 1 Numbers of populations, individuals, organelles and microsatellite loci surveyed in studies published in Molecular Ecology
from January to September 2011
Subject
category
No.
populations
No.
individuals
No.
organelles
No.
microsatellites References
Ecological Genomics N A 186 0 258 Burrell et al. (2011)
Ecological Interactions 3 86 1 17 Foote et al. (2011)
Kinship, Parentage and Behaviour 9 678 1 20 Hua et al. (2011)
23 502 0 10 Qian et al. (2011)
11 211 0 3 Bonckaert et al. (2011)
NA 506 0 7 Tiedemann et al. (2011)
1 333 0 14 Bretman et al. (2011)
NA 779 0 16 Wang & Lu (2011)
NA 254 0 6 Oddou-Muratorio et al. (2011)
NA 771 0 8 Cheron et al. (2011)
NA 204 0 7 Ursprung et al. (2011)
4 253 0 15 Thoss et al. (2011)
NA 337 0 6 Moran & Clark (2011)
NA 12 725 0 8 Christie et al. (2011)
1 102 0 6 While et al. (2011)
Molecular Adaptation 23 1050 0 25 Xhaard et al. (2011)
1 190 0 21 Olsson et al. (2011)
30 853 0 18 Keller et al. (2011)
Phylogeography 2 35 1 16 Kraaijeveld et al. (2011)
14 125 1 10 Lim & Sheldon (2011)
18 170 1 20 Ferrero et al. (2011)
NA 65 0 10 Pepper et al. (2011)
NA 79 1 6 Walter et al. (2011)
1 149 0 15 Hirsch & Maldonado (2011)
17 230 0 9 Kronauer et al. (2011)
NA 864 0 10 Born et al. (2011)
Population and Conservation Genetics 15 689 0 10 Castellanos et al. (2011)
11 1405 1 10 Ozer et al. (2011)
NA 1379 0 11 Cuveliers et al. (2011)
10 310 0 16 Guivier et al. (2011)
10 440 1 23 Lawton et al. (2011)
39 1114 0 6 Mokhtar-Jamai et al. (2011)
NA 153 0 12 Rougeron et al. (2011)
NA 487 0 8 Lye et al. (2011)
3 197 0 103 Li & Merila (2011)
23 123 1 10 Hu et al. (2011)
NA 507 0 7 Criscione et al. (2011)
35 1624 1 10 Andras et al. (2011)
12 312 0 16 Lancaster et al. (2011)
11 319 1 9 Koblmuller et al. (2011)
11 600 1 20 Horne et al. (2011)
8 139 0 7 Kawakami et al. (2011)
3 368 1 22 Agudo et al. (2011)
23 1262 0 8 Bronnenhuber et al. (2011)
235 0 8 Lane & Shine (2011)
4NA 0 15 Luquet et al. (2011)
17 427 0 15 Richter-Boix et al. (2011)
1 125 0 28 Ortego et al. (2011)
5 178 0 9 Chair et al. (2011)
7 192 0 12 Solmsen et al. (2011)
6 476 1 10 van Oppen et al. (2011)
2 520 0 17 Rieux et al. (2011)
10 189 0 8 Chun et al. (2011)
23 337 0 6 Shepherd & Perrie (2011)
11 1824 0 12 Bull et al. (2011)
4EDITORIAL AND RETROSPECTIVE
2011 Blackwell Publishing Ltd
nuclear genes. Similar to the microsatellite studies,
about half of the nuclear gene studies also assay varia-
tion in organellar DNA.
Amplified fragment length polymorphism (AFLP)
studies are rapidly being replaced in Molecular Ecology
by sequence-based markers such as SNPs and restric-
tion site–associated DNA (RAD) sequencing. Nonethe-
less, a substantial number of AFLP studies were
published in Molecular Ecology in 2011 (Fig. 4; Table 4).
The information content of an AFLP fragment is very
low because AFLPs are bi-allelic and dominant. Thus, it
is reassuring that all AFLP studies published in Molecu-
lar Ecology employed >100 loci and most studies
assayed between 200 and 600 loci.
In addition to the 155 studies listed in Tables 1–4, ten
studies were published in Molecular Ecology during
this period that were based solely on one or more
organellar genes. Also, two of the studies that employed
nuclear gene sequence data were based on a single gene.
In total, 12 of 165 studies (7%) included in our survey
are based on data from a single locus. Thus, while single
locus studies are uncommon in the journal, they are not
yet extinct. However, going forward we recommend that
authors base their inferences on multiple loci if at all
possible to ensure that their articles are sent out for
review and are reviewed favourably by referees.
We also examined current standards with respect to
the number of populations and individuals typically
assayed in the different subject categories included in
Molecular Ecology (Figs 5 and 6). Most studies analyse
between 10 and 20 populations and between 200 and 500
individuals. There are two outlier subject categories:
‘Ecological Genomics’ studies typically analyse about
half as many populations as studies from other subject
Table 1 Continued
Subject
category
No.
populations
No.
individuals
No.
organelles
No.
microsatellites References
21 569 0 137 Orozco-terWengel et al. (2011)
NA 192 1 18 Zhu et al. (2011)
16 316 0 8 Schrey et al. (2011b)
NA 94 1 20 Charruau et al. (2011)
10 1132 0 9 Cammen et al. (2011)
16 85 0 15 Karlin et al. (2011)
NA 1287 0 13 Knutsen et al. (2011)
33 516 0 13 Dobata et al. (2011)
14 747 0 8 Winkler et al. (2011)
1 730 0 9 Pluess (2011)
20 478 0 17 Fitzpatrick et al. (2011)
1NA 0 19 Morrissey & Ferguson (2011)
NA 139 0 7 Liebgold et al. (2011)
6 291 0 19 Brekke et al. (2011)
NA 1040 0 9 Hufford et al. (2011)
NA 470 0 8 Schrey et al. (2011a)
1 87 0 24 Grueber et al. (2011)
5 231 1 12 Reichard et al. (2011)
Speciation and Hybridization 29 397 0 9 Chavez et al. (2011)
14 186 1 7 Schmidt et al. (2011)
8 368 1 15 Palma-Silva et al. (2011)
4 591 0 18 Ricca et al. (2011)
25 679 1 13 Bock et al. (2011)
2 28 1 18 Legrand et al. (2011)
2 56 0 25 Buonaccorsi et al. (2011)
NA 731 0 6 Field et al. (2011)
NA 250 1 9 Bohling & Waits (2011)
NA 678 0 12 Cullingham et al. (2011)
NA 1040 1 10 Thierry et al. (2011)
NA 446 1 13 Cabria et al. (2011)
7 102 1 9 Vergilino et al. (2011)
5NA 0 25 Carlon & Lippe (2011)
NA 301 1 6 Pinzon & LaJeunesse (2011)
2 152 1 33 Sacks et al. (2011)
EDITORIAL AND RETROSPECTIVE 5
2011 Blackwell Publishing Ltd
areas (Fig. 5), whereas ‘Kinship, Parentage and Behav-
iour’ studies assay approximately three times more
individuals than studies published in the other subject
categories (Fig. 6). The latter observation is satisfying
because studies in ‘Kinship, Parentage and Behaviour’
typically employ fewer loci than do studies in other cate-
gories, but make up for this by studying much larger
numbers of individuals.
The data presented above are intended to provide
guidance regarding the numbers of populations, indi-
viduals and loci that were perceived by editors and
reviewers as acceptable for publication in Molecular
Ecology. However, we anticipate that these standards
will continue to evolve, with increasingly large data
sets made feasible by improved technology and meth-
odologies. Moreover, sampling strategies and marker
choices should be designed to best address the ques-
tion motivating the study. As we stress in our guide
to authors, our main criterion is that studies utilize
molecular genetic techniques to address consequential
questions in ecology, evolution, behaviour and conser-
vation. If your sampling scheme, molecular genetic
approaches and data analyses strategies are well
designed for investigating an important question in
ecology or evolutionary biology, then your study
stands a very good chance of being published in
Molecular Ecology.
When should you make a complaint?
We handle a large volume of articles and sometimes
make decisions that are unpopular with authors. While
the majority of authors accept an unfavourable decision
and make use of the feedback before submitting else-
where, there are cases where it is worth contacting us
to discuss the decision further. As there is sometimes
confusion on what constitutes a valid reason for revisit-
ing a decision, we have provided some guidance below
regarding when a complaint is likely to be successful
(an earlier version of this piece can be found at http://
www.molecularecologist.com/).
To begin, here are some general suggestions that will
make it more likely that a challenge will be successful.
First, we recommend not contacting the journal imme-
diately after receiving a decision you disagree with, as
the tone of these complaint letters is seldom construc-
tive. Second, avoid using ‘Reply All’ when passing deci-
sion letters to co-authors, particularly if you include
some invective, as these messages sometimes come back
to the journal. Third, before you launch a challenge,
please check with your co-authors, as they may prefer
to submit elsewhere instead.
It is worth noting that complaint letters that attempt
to identify negative reviewers and dismiss their con-
cerns on the grounds that they are prejudiced against
your work are seldom successful. Guesses on reviewer
identity are often wrong, and they also constitute an ad
hominem attack on that person’s integrity. Furthermore,
even if your nemesis did give a signed negative review,
this is not grounds to overturn the decision. The editor
was almost certainly aware of this issue when they
decided to reject your article, and the rejection implies
that the editor either agrees with their criticisms of your
work or else based the rejection on comments of
another referee.
Once you have had a few days to read through the
decision, and you are still convinced that it is unfair,
then compose a carefully worded letter that explains
why the decision needs to be revisited. Be warned that
challenging a decision along the following lines almost
never works out:
– ‘You gave my paper a ‘reject, encourage resubmis-
sion’ decision, but it should have been an ‘acceptance
Table 2 Numbers of populations, individuals, organelles and single nucleotide polymorphisms (SNPs) surveyed in studies pub-
lished in Molecular Ecology from January to September 2011
Subject
category
No.
populations
No.
individuals
No.
organelles
No.
SNPs References
Ecological Genomics 5 576 0 171 Cubillos et al. (2011)
Ecological Interactions 15 105 0 22 Nestmann et al. (2011)
Molecular Adaptation 26 156 0 768 Prunier et al. (2011)
2 186 0 23 Svetec et al. (2011)
Phylogeography 70 70 0 384 Hofinger et al. (2011)
Population and Conservation Genetics 9 466 0 151 Gomaa et al. (2011)
25 725 0 44 057 Gautier & Naves (2011)
Speciation and Hybridization 79 895 0 1536 Wang et al. (2011)
30 604 0 81 Stemshorn et al. (2011)
5 196 0 112 Renaut et al. (2011)
2 152 1 51 Sacks et al. (2011)
6EDITORIAL AND RETROSPECTIVE
2011 Blackwell Publishing Ltd
with minor revisions’. For Molecular Ecology, a reject-
encourage typically indicates that the article needs
extensive changes (potentially including additional
data) and that the editor wants to send it through the
review process again. It is also generally best to
respond to individual reviewer and editor comments
as part of the resubmission rather than to challenge
the decision itself.
– ‘Two of the reviewers loved it and only suggested
minor edits, but Referee 3 was much more negative
and made you reject it’. A decision is not based on an
average of the review recommendations, and if the
comments of Referee 3 convinced the editor that the
article is flawed, no amount of adulation from
reviewers who missed these problems is going to
change that.
‘I accidentally included the wrong dataset analy-
ses conclusions, and this is why the paper was
rejected’. We can only review the materials that have
been sent to us, so please check your manuscript files
carefully before submitting.
‘You published a very similar paper back in 2006, so
it is inconsistent to reject our manuscript now’. The
field is constantly changing and the standards for
publication are always moving higher. If your data
and methods were cutting-edge five years ago, it
Table 3 Numbers of populations, individuals, organelles and nuclear genes surveyed in studies published in Molecular Ecology from
January to September 2011
Subject
category
No.
populations
No.
individuals
No.
organelles
Nuclear
genes References
Ecological Interactions 4 1063 1 1 Tedersoo et al. (2011)
3 64 0 2 Morick et al. (2011)
42 134 0 1 Kennedy et al. (2011)
Molecular Adaptation 15 360 1 5 Atyame et al. (2011)
Phylogeography 14 950 1 2 Fijarczyk et al. (2011)
5 125 1 1 Baird et al. (2011)
19 100 1 1 Cooper et al. (2011)
NA 108 0 3 Gazis et al. (2011)
23 290 1 4 Zhan et al. (2011)
13 161 0 5 Morris-Pocock et al. (2011)
12 81 1 3 Nobre et al. (2011)
3 211 1 1 Triponez et al. (2011)
3 87 1 3 Portik et al. (2011)
NA 85 1 1 Hayward et al. (2011)
11 203 1 2 Fernandez-Mendoza et al. (2011)
13 239 1 2 Schoville et al. (2011)
29 176 0 1 Etter et al. (2011)
45 463 0 5 Roe et al. (2011)
NA 266 1 2 Turmelle et al. (2011)
12 150 1 2 Lohse et al. (2011)
NA 66 1 2 Sarnat & Moreau (2011)
33 170 1 1 Kokita & Nohara (2011)
Population and Conservation Genetics 14 140 0 16 Onge et al. (2011)
50 106 1 1 Douglas et al. (2011)
NA 151 0 2 Le Rouzic et al. (2011)
NA 73 1 3 Welch et al. (2011)
2 127 0 4 McCairns et al. (2011)
Speciation and Hybridization NA 162 1 1 Barrett & Freudenstein (2011)
3 167 1 6 Dyer et al. (2011)
NA 9 0 67 Alamouti et al. (2011)
NA 187 1 12 Brelsford et al. (2011)
40 40 0 18 Bimova et al. (2011)
3 26 1 2 Bird et al. (2011)
6 301 0 10 Ouanes et al. (2011)
2 55 2 17 Wachowiak et al. (2011)
NA 353 0 6 Kiss et al. (2011)
7 776 1 3 Culumber et al. (2011)
EDITORIAL AND RETROSPECTIVE 7
2011 Blackwell Publishing Ltd
saves everyone time if you submit to a more special-
ized journal. Furthermore, even if a manuscript simi-
lar to your own has appeared in the most recent
issue, that accepted manuscript could have other
merits that led to its acceptance. Please also bear in
mind that we have likely already rejected numerous
other similar articles this year, and those decisions
are not made public.
‘We resubmitted our paper, but while the original
reviewers liked the new version, the comments you
received from the new referees made you reject it’.
Molecular Ecology has a policy of only allowing one
‘reject, encourage resubmission’ per article, which
prevents interminable rounds of ‘reject-encourage
resubmission finding new reviewers they find new
problems yet another reject-encourage’. Resubmitted
articles do get accepted about 70%of the time, so
clearly it is possible to prepare a new version that
convinces both the original and the new reviewers
that the manuscript is worth publishing. Lastly, if
none of the original reviewers were able to look
at the resubmission, our only option is to use new
referees.
So when should you challenge a rejection? The reason
that most often leads us to revisit a decision is evidence
that the peer review process was flawed in some way
that unfairly biased the evaluation of your article. For
example, a reviewer might claim that a particular analy-
sis is vital to your study. However, if the analysis is
actually in the article and somehow neither the editor
nor the reviewer noticed it, then certainly the decision
would be revisited. Similarly, if a reviewer convinces
the editor that some aspect of the methods is fundamen-
tally flawed, but the criticism can be shown to be incor-
rect, then it would be worth appealing the decision.
It should be noted that while instances such as the
two described above would be grounds for appeal,
there is no guarantee that the decision will be over-
turned. It might be, for example, that there were other
major flaws in the article that were largely responsible
for its rejection rather than any mistakes made by the
referees or editors. We do occasionally overturn deci-
sions, and if we are convinced by the authors that a
mistake was made in the review process resulting in a
faulty decision, we will either alter the decision or
invite a new version of the article. This is infrequent,
about one in every 50 rejections, but it does happen!
Loren Rieseberg
Chief Editor
(lriesebe@mail.ubc.ca)
Tim Vines
Managing Editor
(managing.editor@molecol.com)
Nolan Kane
News and Views Editor
(nckane@gmail.com)
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Table 4 Numbers of populations, individuals, organelles and amplified fragment length polymorphisms (AFLPs) surveyed in stud-
ies published in Molecular Ecology from January to September 2011
Subject
category
No.
populations
No.
individuals
No.
organelles AFLPs References
Ecological Genomics 8 258 0 609 Midamegbe et al. (2011)
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8EDITORIAL AND RETROSPECTIVE
2011 Blackwell Publishing Ltd
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differentiation of Aucoumea klaineana.Molecular Ecology,20,
131–142.
Brekke P, Bennett PM, Santure AW, Ewen JG (2011) High
genetic diversity in the remnant island population of hihi
and the genetic consequences of re-introduction. Molecular
Ecology,20, 29–45.
Brelsford A, Mila B, Irwin DE (2011) Hybrid origin of
Audubon’s warbler. Molecular Ecology,20, 2380–2389.
Bretman A, Rodriguez-Munoz R, Walling C, Slate J, Tregenza
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avoidance in a wild insect population. Molecular Ecology,20,
3045–3055.
Bronnenhuber JE, Dufour BA, Higgs DM, Heath DD (2011)
Dispersal strategies, secondary range expansion and invasion
genetics of the nonindigenous round goby, Neogobius
melanostomus, in Great Lakes tributaries. Molecular Ecology,
20, 1845–1859.
Bull RAS, Cushman SA, Mace R et al. (2011) Why replication
is important in landscape genetics: American black bear in
the Rocky Mountains. Molecular Ecology,20, 1092–1107.
Buonaccorsi VP, Narum SR, Karkoska KA et al. (2011)
Characterization of a genomic divergence island between
black-and-yellow and gopher Sebastes rockfishes.Molecular
Ecology,20, 2603–2618.
Burrell AM, Taylor KG, Williams RJ et al. (2011) A
comparative genomic map for Caulanthus amplexicaulis and
related species (Brassicaceae). Molecular Ecology,20, 784–798.
Cabria MT, Michaux JR, Gomez-Moliner BJ et al. (2011)
Bayesian analysis of hybridization and introgression between
the endangered european mink (Mustela lutreola) and
the polecat (Mustela putorius). Molecular Ecology,20, 1176–1190.
Cammen K, Hoffman JI, Knapp LA, Harwood J, Amos W
(2011) Geographic variation of the major histocompatibility
complex in Eastern Atlantic grey seals (Halichoerus grypus).
Molecular Ecology,20, 740–752.
Carlon DB, Lippe C (2011) Estimation of mating systems in
Short and Tall ecomorphs of the coral Favia fragum.Molecular
Ecology,20, 812–828.
Castellanos MC, Alcantara JM, Rey PJ, Bastida JM (2011) Intra-
population comparison of vegetative and floral trait
heritabilities estimated from molecular markers in wild
Aquilegia populations. Molecular Ecology,20, 3513–3524.
Chair H, Duroy PO, Cubry P, Sinsin B, Pham JL (2011) Impact
of past climatic and recent anthropogenic factors on wild
yam genetic diversity. Molecular Ecology,20, 1612–1623.
Charruau P, Fernandes C, Orozco-Ter Wengel P et al. (2011)
Phylogeography, genetic structure and population
divergence time of cheetahs in Africa and Asia: evidence for
long-term geographic isolates. Molecular Ecology,20, 706–724.
Chavez AS, Saltzberg CJ, Kenagy GJ (2011) Genetic and
phenotypic variation across a hybrid zone between
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Ecology,20, 3350–3366.
Cheron B, Monnin T, Federici P, Doums C (2011) Variation in
patriline reproductive success during queen production in
orphaned colonies of the thelytokous ant Cataglyphis cursor.
Molecular Ecology,20, 2011–2022.
Christie MR, Marine ML, Blouin MS (2011) Who are the
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sources of gene flow into a wild population. Molecular
Ecology,20, 1263–1276.
Chun YJ, Le Corre V, Bretagnolle F (2011) Adaptive divergence
for a fitness-related trait among invasive Ambrosia
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1378–1388.
Colbeck GJ, Turgeon J, Sirois P, Dodson JJ (2011) Historical
introgression and the role of selective vs. neutral processes
in structuring nuclear genetic variation (AFLP) in a
circumpolar marine fish, the capelin (Mallotus villosus).
Molecular Ecology,20, 1976–1987.
Cooper SJB, Harvey MS, Saint KM, Main BY (2011) Deep
phylogeographic structuring of populations of the trapdoor
spider Moggridgea tingle (Migidae) from southwestern
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Molecular Ecology,20, 3219–3236.
Cox K, Broeck AV, Van Calster H, Mergeay J (2011)
Temperature-related natural selection in a wind-pollinated
tree across regional and continental scales. Molecular Ecology,
20, 2724–2738.
Criscione CD, Vilas R, Paniagua E, Blouin MS (2011) More
than meets the eye: detecting cryptic microgeographic
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Molecular Ecology,20, 2510–2524.
Croucher PJP, Oxford GS, Lam A, Gillespie RG (2011)
Stabilizing selection maintains exuberant colour
polymorphism in the spider Theridion californicum (Araneae,
Theridiidae). Molecular Ecology,20, 206–218.
EDITORIAL AND RETROSPECTIVE 9
2011 Blackwell Publishing Ltd
Cubillos FA, Billi E, Zorgo E et al. (2011) Assessing the
complex architecture of polygenic traits in diverged yeast
populations. Molecular Ecology,20, 1401–1413.
Cullingham CI, Cooke JEK, Dang S et al. (2011) Mountain pine
beetle host-range expansion threatens the boreal forest.
Molecular Ecology,20, 2157–2171.
Culumber ZW, Fisher HS, Tobler M et al. (2011) Replicated
hybrid zones of Xiphophorus swordtails along an elevational
gradient. Molecular Ecology,20, 342–356.
Cuveliers EL, Volckaert FAM, Rijnsdorp AD, Larmuseau
MHD, Maes GE (2011) Temporal genetic stability and high
effective population size despite fisheries-induced life-history
trait evolution in the North Sea sole. Molecular Ecology,20,
3555–3568.
Dobata S, Sasaki T, Mori H et al. (2011) Persistence of the
single lineage of transmissible ‘social cancer’ in an asexual
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Douglas NA, Wall WA, Xiang QY et al. (2011) Recent
vicariance and the origin of the rare, edaphically specialized
Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from
phylogenetic and coalescent analyses. Molecular Ecology,20,
2901–2915.
Dyer KA, Burke C, Jaenike J (2011) Wolbachia-mediated
persistence of mtDNA from a potentially extinct species.
Molecular Ecology,20, 2805–2817.
Etter RJ, Boyle EE, Glazier A et al. (2011) Phylogeography of a
pan-Atlantic abyssal protobranch bivalve: implications for
evolution in the Deep Atlantic. Molecular Ecology,20, 829–843.
Fernandez-Mendoza F, Domaschke S, Garcia MA et al. (2011)
Population structure of mycobionts and photobionts of the
widespread lichen Cetraria aculeata.Molecular Ecology,20,
1208–1232.
Ferrero ME, Blanco-Aguiar JA, Lougheed SC et al. (2011)
Phylogeography and genetic structure of the red-legged
partridge (Alectoris rufa): more evidence for refugia within
the Iberian glacial refugium. Molecular Ecology,20, 2628–
2642.
Field DL, Ayre DJ, Whelan RJ, Young AG (2011) The
importance of pre-mating barriers and the local demographic
context for contemporary mating patterns in hybrid zones of
Eucalyptus aggregata and Eucalyptus rubida.Molecular Ecology,
20, 2367–2379.
Fijarczyk A, Nadachowska K, Hofman S et al. (2011) Nuclear
and mitochondrial phylogeography of the European fire-
bellied toads Bombina bombina and Bombina variegata supports
their independent histories. Molecular Ecology,20, 3381–3398.
Fischer MC, Foll M, Excoffier L, Heckel G (2011) Enhanced
AFLP genome scans detect local adaptation in high-altitude
populations of a small rodent (Microtus arvalis). Molecular
Ecology,20, 1450–1462.
Fitzpatrick JM, Carlon DB, Lippe C, Robertson DR (2011) The
West Pacific diversity hotspot as a source or sink for new
species? Population genetic insights from the Indo-Pacific
parrotfish Scarus rubroviolaceus. Molecular Ecology,20, 219–
234.
Foote AD, Vilstrup JT, de Stephanis R et al. (2011) Genetic
differentiation among North Atlantic killer whale
populations. Molecular Ecology,20, 629–641.
Gautier M, Naves M (2011) Footprints of selection in the
ancestral admixture of a New World Creole cattle breed.
Molecular Ecology,20, 3128–3143.
Gazis R, Rehner S, Chaverri P (2011) Species delimitation in
fungal endophyte diversity studies and its implications in
ecological and biogeographic inferences. Molecular Ecology,
20, 3001–3013.
Gomaa NH, Montesinos-Navarro A, Alonso-Blanco C, Pico FX
(2011) Temporal variation in genetic diversity and effective
population size of Mediterranean and subalpine Arabidopsis
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Gonthier P, Garbelotto M (2011) Amplified fragment length
polymorphism and sequence analyses reveal massive gene
introgression from the European fungal pathogen
Heterobasidion annosum into its introduced congener H.
irregulare.Molecular Ecology,20, 2756–2770.
Groot AT, Classen A, Inglis O et al. (2011) Genetic
differentiation across North America in the generalist moth
Heliothis virescens and the specialist H. subflexa.Molecular
Ecology,20, 2676–2692.
Grueber CE, Waters JM, Jamieson IG (2011) The imprecision of
heterozygosity-fitness correlations hinders the detection of
inbreeding and inbreeding depression in a threatened
species. Molecular Ecology,20, 67–79.
Guivier E, Galan M, Chaval Y et al. (2011) Landscape genetics
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the epidemiology of Puumala hantavirus. Molecular Ecology,
20, 3569–3583.
Hayward A, McMahon DP, Kathirithamby J (2011) Cryptic
diversity and female host specificity in a parasitoid where
the sexes utilize hosts from separate orders. Molecular
Ecology,20, 1508–1528.
Hirsch BT, Maldonado JE (2011) Familiarity breeds progeny:
sociality increases reproductive success in adult male
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419.
Hofinger BJ, Russell JR, Bass CG et al. (2011) An exceptionally
high nucleotide and haplotype diversity and a signature of
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revealed by allele mining and phylogenetic analyses of
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Horne JB, Momigliano P, Welch DJ, Newman SJ, van
Herwerden L (2011) Limited ecological population
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tropical inshore marine fish (Eleutheronema tetradactylum:
Polynemidae). Molecular Ecology,20, 2291–2306.
Hu Y, Guo Y, Qi DW et al. (2011) Genetic structuring and
recent demographic history of red pandas (Ailurus fulgens)
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Molecular Ecology,20, 2662–2675.
Hua PY, Zhang LB, Zhu GJ et al. (2011) Hierarchical polygyny
in multiparous lesser flat-headed bats. Molecular Ecology,20,
3669–3680.
Hufford MB, Gepts P, Ross-Ibarra J (2011) Influence of cryptic
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Molecular Ecology,20, 46–55.
Humphries EM, Winker K (2011) Discord reigns among
nuclear, mitochondrial and phenotypic estimates of
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Molecular Ecology,20, 573–583.
Irwin DE, Irwin JH, Smith TB (2011) Genetic variation and
seasonal migratory connectivity in Wilson’s warblers
(Wilsonia pusilla): species-level differences in nuclear DNA
10 EDITORIAL AND RETROSPECTIVE
2011 Blackwell Publishing Ltd
between western and eastern populations. Molecular Ecology,
20, 3102–3115.
Karlin EF, Andrus RE, Boles SB, Shaw AJ (2011) One haploid
parent contributes 100%of the gene pool for a widespread
species in northwest North America. Molecular Ecology,20,
753–767.
Kawakami T, Morgan TJ, Nippert JB et al. (2011) Natural
selection drives clinal life history patterns in the perennial
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20, 2318–2328.
Keller I, Taverna A, Seehausen O (2011) Evidence of neutral
and adaptive genetic divergence between European trout
populations sampled along altitudinal gradients. Molecular
Ecology,20, 1888–1904.
Kennedy AH, Taylor DL, Watson LE (2011) Mycorrhizal
specificity in the fully mycoheterotrophic Hexalectris Raf.
(Orchidaceae: Epidendroideae). Molecular Ecology,20, 1303–
1316.
Kiss L, Pintye A, Kovacs GM et al. (2011) Temporal isolation
explains host-related genetic differentiation in a group of
widespread mycoparasitic fungi. Molecular Ecology,20, 1492–
1507.
Knutsen H, Olsen EM, Jorde PE et al. (2011) Are low but
statistically significant levels of genetic differentiation in
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coastal Atlantic cod. Molecular Ecology,20, 768–783.
Koblmuller S, Salzburger W, Obermuller B et al. (2011)
Separated by sand, fused by dropping water: habitat barriers
and fluctuating water levels steer the evolution of rock-
dwelling cichlid populations in Lake Tanganyika. Molecular
Ecology,20, 2272–2290.
Kokita T, Nohara K (2011) Phylogeography and historical
demography of the anadromous fish Leucopsarion petersii in
relation to geological history and oceanography around the
Japanese Archipelago. Molecular Ecology,20, 143–164.
Kraaijeveld K, Franco P, De Knijff P, Stouthamer R, Van
Alphen JJM (2011) Clonal genetic variation in a Wolbachia-
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sex? Molecular Ecology,20, 3644–3652.
Kronauer DJC, O’Donnell S, Boomsma JJ, Pierce NE (2011)
Strict monandry in the ponerine army ant genus Simopelta
suggests that colony size and complexity drive mating
system evolution in social insects. Molecular Ecology,20, 420–
428.
Lancaster ML, Taylor AC, Cooper SJB, Carthew SM (2011)
Limited ecological connectivity of an arboreal marsupial
across a forest plantation landscape despite apparent
resilience to fragmentation. Molecular Ecology,20, 2258–
2271.
Lane A, Shine R (2011) Intraspecific variation in the direction
and degree of sex-biased dispersal among sea-snake
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Lawton RJ, Messmer V, Pratchett MS, Bay LK (2011) High
gene flow across large geographic scales reduces extinction
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Molecular Ecology,20, 3584–3598.
Le Rouzic A, Ostbye K, Klepaker TO et al. (2011) Strong and
consistent natural selection associated with armour reduction
in sticklebacks. Molecular Ecology,20, 2483–2493.
Legrand D, Chenel T, Campagne C, Lachaise D, Cariou ML
(2011) Inter-island divergence within Drosophila mauritiana,a
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speciation in progress? Molecular Ecology,20, 2787–2804.
Li MH, Merila J (2011) Population differences in levels of
linkage disequilibrium in the wild. Molecular Ecology,20,
2916–2928.
Liebgold EB, Brodie ED, Cabe PR (2011) Female philopatry
and male-biased dispersal in a direct-developing
salamander, Plethodon cinereus.Molecular Ecology,20, 249–
257.
Lim HC, Sheldon FH (2011) Multilocus analysis of the
evolutionary dynamics of rainforest bird populations in
Southeast Asia. Molecular Ecology,20, 3414–3438.
Lohse K, Nicholls JA, Stone GN (2011) Inferring the
colonization of a mountain range-refugia vs. nunatak
survival in high alpine ground beetles. Molecular Ecology,20,
394–408.
Luquet E, David P, Lena JP et al. (2011) Heterozygosity-fitness
correlations among wild populations of European tree frog
(Hyla arborea) detect fixation load. Molecular Ecology,20,
1877–1887.
Lye GC, Lepais O, Goulson D (2011) Reconstructing
demographic events from population genetic data: the
introduction of bumblebees to New Zealand. Molecular
Ecology,20, 2888–2900.
McCairns RJS, Bourget S, Bernatchez L (2011) Putative causes
and consequences of MHC variation within and between
locally adapted stickleback demes. Molecular Ecology,20,
486–502.
Midamegbe A, Vitalis R, Malausa T et al. (2011) Scanning the
European corn borer (Ostrinia spp.) genome for adaptive
divergence between host-affiliated sibling species. Molecular
Ecology,20, 1414–1430.
Mokhtar-Jamai K, Pascual M, Ledoux JB et al. (2011) From
global to local genetic structuring in the red gorgonian
Paramuricea clavata: the interplay between oceanographic
conditions and limited larval dispersal. Molecular Ecology,20,
3291–3305.
Moran EV, Clark JS (2011) Estimating seed and pollen
movement in a monoecious plant: a hierarchical Bayesian
approach integrating genetic and ecological data. Molecular
Ecology,20, 1248–1262.
Morick D, Krasnov BR, Khokhlova IS, Gottlieb Y, Harrus S
(2011) Investigation of Bartonella acquisition and
transmission in Xenopsylla ramesis fleas (Siphonaptera:
Pulicidae). Molecular Ecology,20, 2864–2870.
Morris-Pocock JA, Anderson DJ, Friesen VL (2011)
Mechanisms of global diversification in the brown booby
(Sula leucogaster) revealed by uniting statistical
phylogeographic and multilocus phylogenetic methods.
Molecular Ecology,20, 2835–2850.
Morrissey MB, Ferguson MM (2011) Individual variation in
movement throughout the life cycle of a stream-dwelling
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Nestmann S, Rajicic TS, Dehmer KJ et al. (2011) Plant species
diversity and composition of experimental grasslands affect
genetic differentiation of Lolium perenne populations.
Molecular Ecology,20, 2188–2203.
Nobre T, Fernandes C, Boomsma JJ, Korb J, Aanen DK (2011)
Farming termites determine the genetic population structure
of Termitomyces fungal symbionts. Molecular Ecology,20,
2023–2033.
EDITORIAL AND RETROSPECTIVE 11
2011 Blackwell Publishing Ltd
Nunes VL, Beaumont MA, Butlin RK, Paulo OS (2011)
Multiple approaches to detect outliers in a genome scan for
selection in ocellated lizards (Lacerta lepida) along an
environmental gradient. Molecular Ecology,20, 193–205.
Oddou-Muratorio S, Klein EK, Vendramin GG, Fady B (2011)
Spatial vs. temporal effects on demographic and genetic
structures: the roles of dispersal, masting and differential
mortality on patterns of recruitment in Fagus sylvatica.
Molecular Ecology,20, 1997–2010.
Olsson M, Pauliny A, Wapstra E et al. (2011) Sexual
differences in telomere selection in the wild. Molecular
Ecology,20, 2085–2099.
Onge KRS, Kallman T, Slotte T, Lascoux M, Palme AE (2011)
Contrasting demographic history and population structure in
Capsella rubella and Capsella grandiflora, two closely related
species with different mating systems. Molecular Ecology,20,
3306–3320.
van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM,
Cooper TF (2011) The role of deep reefs in shallow reef
recovery: an assessment of vertical connectivity in a
brooding coral from west and east Australia. Molecular
Ecology,20, 1647–1660.
Orozco-terWengel P, Corander J, Schlotterer C (2011)
Genealogical lineage sorting leads to significant, but
incorrect Bayesian multilocus inference of population
structure. Molecular Ecology,20, 1108–1121.
Ortego J, Yannic G, Shafer ABA et al. (2011) Temporal
dynamics of genetic variability in a mountain goat (Oreamnos
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Ouanes K, Bahri-Sfar L, Ben Hassine OK, Bonhomme F (2011)
Expanding hybrid zone between Solea aegyptiaca and Solea
senegalensis: genetic evidence over two decades. Molecular
Ecology,20, 1717–1728.
Ozer F, Gellerman H, Ashley MV (2011) Genetic impacts of
Anacapa deer mice reintroductions following rat eradication.
Molecular Ecology,20, 3525–3539.
Palma-Silva C, Wendt T, Pinheiro F et al. (2011) Sympatric
bromeliad species (Pitcairnia spp.) facilitate tests of
mechanisms involved in species cohesion and reproductive
isolation in Neotropical inselbergs. Molecular Ecology,20,
3185–3201.
Pepper M, Fujita MK, Moritz C, Keogh JS (2011) Palaeoclimate
change drove diversification among isolated mountain
refugia in the Australian arid zone. Molecular Ecology,20,
1529–1545.
Pinzon JH, LaJeunesse TC (2011) Species delimitation of
common reef corals in the genus Pocillopora using nucleotide
sequence phylogenies, population genetics and symbiosis
ecology. Molecular Ecology,20, 311–325.
Pluess AR (2011) Pursuing glacier retreat: genetic structure of a
rapidly expanding Larix decidua population. Molecular
Ecology,20, 473–485.
Portik DM, Bauer AM, Jackman TR (2011) Bridging the gap:
western rock skinks (Trachylepis sulcata) have a short history
in South Africa. Molecular Ecology,20, 1744–1758.
Prunier J, Laroche J, Beaulieu J, Bousquet J (2011) Scanning the
genome for gene SNPs related to climate adaptation and
estimating selection at the molecular level in boreal black
spruce. Molecular Ecology,20, 1702–1716.
Qian ZQ, Schluns H, Schlick-Steiner BC et al. (2011)
Intraspecific support for the polygyny-vs.-polyandry
hypothesis in the bulldog ant Myrmecia brevinoda.Molecular
Ecology,20, 3681–3691.
Reichard M, Bryja J, Polacik M, Smith C (2011) No evidence
for host specialization or host-race formation in the
European bitterling (Rhodeus amarus), a fish that parasitizes
freshwater mussels. Molecular Ecology,20, 3631–3643.
Renaut S, Nolte AW, Rogers SM, Derome N, Bernatchez L
(2011) SNP signatures of selection on standing genetic
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Ricca M, Szovenyi P, Temsch EM, Johnson MG, Shaw AJ
(2011) Interploidal hybridization and mating patterns in the
Sphagnum subsecundum complex. Molecular Ecology,20, 3202–
3218.
Richter-Boix A, Quintela M, Segelbacher G, Laurila A (2011)
Genetic analysis of differentiation among breeding ponds
reveals a candidate gene for local adaptation in Rana arvalis.
Molecular Ecology,20, 1582–1600.
Rieux A, Halkett F, de Bellaire LD et al. (2011) Inferences on
pathogenic fungus population structures from microsatellite
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Molecular Ecology,20, 1661–1674.
Roe AD, Rice AV, Coltman DW, Cooke JEK, Sperling FAH
(2011) Comparative phylogeography, genetic differentiation
and contrasting reproductive modes in three fungal
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Ecology,20, 584–600.
Rougeron V, Banuls AL, Carme B et al. (2011) Reproductive
strategies and population structure in Leishmania: substantial
amount of sex in Leishmania Viannia guyanensis.Molecular
Ecology,20, 3116–3127.
Sacks BN, Moore M, Statham MJ, Wittmer HU (2011) A
restricted hybrid zone between native and introduced red
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barriers and competitive exclusion. Molecular Ecology,20,
326–341.
Sarnat EM, Moreau CS (2011) Biogeography and
morphological evolution in a Pacific island ant radiation.
Molecular Ecology,20, 114–130.
Schmidt DJ, Bond NR, Adams M, Hughes JM (2011)
Cytonuclear evidence for hybridogenetic reproduction in
natural populations of the Australian carp gudgeon
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Schoville SD, Stuckey M, Roderick GK (2011) Pleistocene origin
and population history of a neoendemic alpine butterfly.
Molecular Ecology,20, 1233–1247.
Schrey AW, Fox AM, Mushinsky HR, McCoy ED (2011a) Fire
increases variance in genetic characteristics of Florida Sand
Skink (Plestiodon reynoldsi) local populations. Molecular
Ecology,20, 56–66.
Schrey AW, Grispo M, Awad M et al. (2011b) Broad-scale
latitudinal patterns of genetic diversity among native
European and introduced house sparrow (Passer domesticus)
populations. Molecular Ecology,20, 1133–1143.
Shepherd LD, Perrie LR (2011) Microsatellite DNA analyses of
a highly disjunct New Zealand tree reveal strong
differentiation and imply a formerly more continuous
distribution. Molecular Ecology,20, 1389–1400.
Solmsen N, Johannesen J, Schradin C (2011) Highly
asymmetric fine-scale genetic structure between sexes of
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African striped mice and indication for condition dependent
alternative male dispersal tactics. Molecular Ecology,20, 1624–
1634.
Stemshorn KC, Reed FA, Nolte AW, Tautz D (2011) Rapid
formation of distinct hybrid lineages after secondary contact
of two fish species (Cottus sp.). Molecular Ecology,20, 1475–
1491.
Svetec N, Werzner A, Wilches R et al. (2011) Identification of
X-linked quantitative trait loci affecting cold tolerance in
Drosophila melanogaster and fine mapping by selective sweep
analysis. Molecular Ecology,20, 530–544.
Tedersoo L, Bahram M, Jairus T et al. (2011) Spatial structure
and the effects of host and soil environments on
communities of ectomycorrhizal fungi in wooded savannas
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Molecular Ecology,20, 3071–3080.
Thierry M, Becker N, Hajri A et al. (2011) Symbiont diversity
and non-random hybridization among indigenous (Ms) and
invasive (B) biotypes of Bemisia tabaci.Molecular Ecology,20,
2172–2187.
Thoss M, Ilmonen P, Musolf K, Penn DJ (2011) Major
histocompatibility complex heterozygosity enhances
reproductive success. Molecular Ecology,20, 1546–1557.
Tiedemann R, Paulus KB, Havenstein K et al. (2011) Alien eggs
in duck nests: brood parasitism or a help from Grandma?
Molecular Ecology,20, 3237–3250.
Triponez Y, Buerki S, Borer M et al. (2011) Discordances
between phylogenetic and morphological patterns in alpine
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lineages in postglacial Europe. Molecular Ecology,20, 2442–
2463.
Turmelle AS, Kunz TH, Sorenson MD (2011) A tale of two
genomes: contrasting patterns of phylogeographic structure
in a widely distributed bat. Molecular Ecology,20, 357–375.
Ursprung E, Ringler M, Jehle R, Hodl W (2011) Strong
male male competition allows for nonchoosy females: high
levels of polygynandry in a territorial frog with paternal
care. Molecular Ecology,20, 1759–1771.
Vergilino R, Markova S, Ventura M, Manca M, Dufresne F
(2011) Reticulate evolution of the Daphnia pulex complex as
revealed by nuclear markers. Molecular Ecology,20, 1191–
1207.
Wachowiak W, Palme AE, Savolainen O (2011) Speciation
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P. uliginosa (N.) and P. sylvestris (L.). Molecular Ecology,20,
1729–1743.
Walter RP, Blum MJ, Snider SB et al. (2011) Isolation and
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Data accessibility
All data for this manuscript are given in Tables 1–4.
EDITORIAL AND RETROSPECTIVE 13
2011 Blackwell Publishing Ltd
We are very grateful to the large number of individuals who have contributed to the field of molecular ecology by reviewing
manuscripts for the journal. The following list contains people who reviewed articles for Molecular Ecology between 1 November
2010 and 15 October 2011.
Marco Abbiati
Patrick Abbot
Cathryn L. Abbott
Yoshihisa Abe
Maria Ana Aboim
Karina Acevedo-Whitehouse
Guillauve Achaz
Silvia Gonzalez Acinas
Jennifer R. Adams
Mark Adams
Sina Adl
Peter H. Adler
Aneil Agrawal
Andres Aguilar
O. Mario Aguilar
Ramiro Aguilar
Gabriela Aguileta
Robert Ahern
Dirk Ahrens
Sally N. Aitken
Mikael Akesson
Joshua Akey
Ihsan A. Al-Shehbaz
Cedric Alaux
Dirk Albach
Rafael G. Albaladejo
Filipe Alberto
Miguel Alcaide
Alexandre Aleixo
Jussi S. Alho
Sajid Ali
Robin Allaby
Dominique Allaine
Franc¸ois Allal
Geraldine A. Allen
Fred W. Allendorf
Dilara Ally
S. Elizabeth Alter
David Althoff
Diego F. Alvarado-S.
Nadir Alvarez
Paulo C. Alves
Anthony S. Amend
William Amos
Liselotte W. Andersen
Corey D. Anderson
Frank Anderson
Joseph H. Anderson
Kirk E. Anderson
Leif Andersson
Malte Andersson
Peter Andolfatto
Carl Andre
´
Nikos Andreakis
Marco Andrello
Rose L. Andrew
Cecile Ane
Lisa Angeloni
Bernard Angers
Stephen Ansell
Tiago Antao
Agostinho Antunes
Jose
´M. Aparicio
Joseph J. Apodaca
Julien April
Smita Apte
Hitoshi Araki
Frederick I. Archer
Elizabeth Archie
William R. Ardren
Paul Arens
Dave Armitage
Jean-Francois Arnaud
Sophie Arnaud-Haond
Matt Arnegard
Michael L. Arnold
J. W. (Pim) Arntzen
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John Avise
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Debra Ayres
Abdu F. Azad
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Wieslaw Babik
Roberto Bacilieri
Niclas Backstrom
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C. F. Baer
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`res-Urbany
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John Bailey
John Baines
Andrew Baird
Allan J. Baker
Robert Baker
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N. Balkenhol
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˜uls
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Martin J. Barbetti
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¨ren Bolte
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´line Born
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´rez
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Elizabeth G. Boulding
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Sarah Boyer
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´cia Brito
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Lyn G. Cook
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Arielle Cooley
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W. James Cooper
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Paolo Cortesi
Jean-Franc¸ois Cosson
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´e
Aure
´lie Coulon
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Kelly D. Craven
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Erika Crispo
Melania E. A. Cristescu
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Tom Cross
Shannan Crow
Robert H. Cruickshank
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Mitchell Cruzan
Francisco Cubillos
Yujun Cui
Catherine I. Cullingham
Molly Cummings
Larry Curtis
Thomas Curtis
Asher D. Cutter
Fernando Mendonc¸a d’Horta
Anders Goncalves da Silva
Jeffrey M. DaCosta
Love Dale
´n
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Anne C. Dalziel
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Chris Darimont
John A. Darling
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Patrice David
William S. Davidson
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Michael Dawson
Marta De Barba
Henrik H. de Fine Licht
Gerdien de Jong
Guillaume de Lafontaine
Thierry De Meeu
ˆs
Sophie de Proce
Kevin de Queiroz
L. de Souza Rocha
Bruce E. Deagle
Wilhelm DeBeer
Ellen Decaestecker
Eric DeChaine
Bernd Degen
Jeremiah Degenhardt
James Degnan
Sandie Degnan
Jacob F. Degner
Mary Delany
Lynda Delph
Stefan Dennenmoser
Lou Densmore
Nicolas Derome
David Des Marais
Michael K. DeSalvo
Philippe Deschamps
Aure
´lie Deveau
Se
´bastien Devillard
Andrew DeWoody
Jennifer DeWoody
Randy DeYoung
Joseph DiBattista
Carl Dick
Christopher Dick
Ian Dickie
Timothy A. Dickinson
Andreas Diefenbach
Onno E. Diekmann
Li Ding
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Niels Dingemanse
Jose Alexandre F. Diniz-Filho
Me
´lanie Dionne
Sergey Dobretsov
F. S. Dobson
Stephen Dobson
Julian Dodson
Isabelle Domaizon
David Douds
Angela E. Douglas
Norman A. Douglas
Greg Douhan
Claudie Doums
Tom Dowling
Christine Dreyer
Sergei V. Drovetski
Sylvain Dubey
Pierre Duchesne
Thomas Duda
Siobain Duffy
France Dufresne
Alex J. Dumbrell
Jerome Duminil
Susie Dunham
Walt Dunlap
Peter Dunn
Stacey J. Dunn
Glenn J. Dunshea
Micah Dunthorn
Isabelle Dupanloup
Lise Dupont
Anne Duputie
´
Eric Y. Durand
Jean-Dominique Durand
Olivier Duron
Cyril Dutech
David Duvernell
Rodney Dyer
Jacqualyn Eales
Dieter Ebert
Andrew Eckert
Lutz Eckstein
Alexis Edwards
Christine Edwards
Danielle L. Edwards
Ivan Edwards
Owain Edwards
Scott V. Edwards
Scott P. Egan
Keith Egger
Luis Eguiarte
Pernille B. Eidesen
Sigurd Einum
Eduardo Eizirik
Robert Ekblom
Barbara Ekbom
Jan Ekman
Mogbel A. A. El-Niweiri
Mark Eldridge
Willy Eldridge
Marianne Elias
Hans Ellegren
Ryan Ellingson
Jonathan Ellis
Chris Ellison
Norm Ellstrand
Kathryn R. Elmer
James Elser
Kevin Emerson
Virginia J. Emery
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Philip England
Je
´ro
ˆme Enjalbert
Richard Ennos
Laura S. Epp
Clinton Epps
Nathalie Escaravage
Marcial Escudero
Anahı
´Espı
´ndola
Genoveva Esteban
Pedro J. Esteves
Pascal Eusemann
Guillaume Evanno
Melissa Evans
Tyler G. Evans
Warren Ewens
Ron I. Eytan
Anna Fabiani
Bruno Fady
Steve Fain
Dan Faith
Gwen Falony
Leanne Faulks
Cecile Fauvelot
Guido Favia
J. C. Fay
Aron J. Fazekas
Paul Fearnhead
Jeffrey Feder
Vadim Fedorov
Edward J. Feil
Heike Feldhaar
Kevin A. Feldheim
Stephane Fenart
Brian Fenton
Brock Fenton
Juan F. Ferna
´ndez-Manjarre
´s
Fernando Fernandez-
Mendoza
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Gentile F. Ficetola
David L. Field
Christian C. Figueroa
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˚
Ian Fleming
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Vera G. Fonseca
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Brian Ford-Lloyd
Matthew L. Forister
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Lars Forsberg
Par Forslund
Marie-Josee Fortin
William Foster
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Alexandre Fournier-Level
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Thales Renato O. de Freitas
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¨rgen Gadau
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´a
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´zsef Geml
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´lez-Martı
´nez
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´lez-Rodrı
´guez
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´lez-Tizo
´n
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Tamar Goulet
Dave Goulson
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¨ner
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¨r Ingvarsson
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´phane Joost
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¨rgens
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¨la
¨inen
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´
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¨l J. Kergoat
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¨nstner
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Luc Lens
Tobias L. Lenz
Jennifer Leonard
Olivier Lepais
Matthieu Leray
Enrique P. Lessa
Michael P. Lesser
Harilaos Lessios
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Mia Levine
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Meng-Hua Li
Miriam Liedvogel
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Celeste Linde
Anna Lindholm
Dan Lindner
Catherine Linnen
Katrin Linse
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Dorn Lisa
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T. J. Little
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Liang Liu
Shu-Sheng Liu
Curt Lively
Ana Llopart
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Julie Lockwood
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Tristan Long
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Carlos Lopez-Vaamonde
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Stephen C. Lougheed
Ed Louis
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Irby Lovette
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Benjamin Lowe
Winsor Lowe
David Lowry
Hugh Loxdale
Jeffrey D. Lozier
Xin Lu
Yingqing Lu
Kay Lucek
Arne Ludwig
Dieter Lukas
Vimoksalehi Lukoschek
Max Lundberg
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Emilien Luquet
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Julien Mainguy
Hannu I. Ma
¨kinen
Anna Malacrida
Jason Malaney
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´s E. Maldonado
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Jim Mallet
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Bohumil Manda
´k
Jennifer Mandel
Ste
´phanie Manel
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´Martı
´nez-de la Puente
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´nica Martı
´nez-Ferna
´ndez
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´nez-Romero
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˜igo Martı
´nez-Solano
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´lia Martı
´nkova
´
Vincent G. Martinson
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Several animal species have recently been shown to have hybrid origins, but no avian examples have been documented with molecular evidence. We investigate whether the Audubon’s warbler (Dendroica auduboni), one of four visually distinct species in the yellow-rumped warbler complex, has originated through hybridization between two other species in this group, the myrtle warbler (D. coronata) and black-fronted warbler (D. nigrifrons). Analysis of nuclear amplified fragment length polymorphism (AFLP) and sequence markers shows that Audubon’s warblers are genetically intermediate and carry a mixture of alleles otherwise found only in one or the other of their putative parental species. Audubon’s warblers also carry two deeply divergent mitochondrial DNA lineages, each shared with only one putative parental form. Broad clines between Audubon’s and black-fronted warblers in AFLP markers call into question the validity of these two forms as full species; nevertheless, our results suggest that the Audubon’s warbler probably originated through hybridization between two long-diverged species. It is likely that more cases of avian species of hybrid origin will be revealed by surveys of variation in nuclear DNA and other traits.
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Adaptation to environment is the cornerstone of ecological genetics. The subject of this study is a wild relative of the sequenced and annotated model plant species, Arabidopsis thaliana. Caulanthus amplexicaulis var. barbarae lives on serpentine soils, known for high concentrations of heavy metals and low concentrations of essential plant macronutrients, and provides a compelling example of an organism’s adaptation to environment. We constructed an F2 linkage map, using a cross to the nonserpentine sister taxon, C. amplexicaulis var. amplexicaulis. C. amplexicaulis is a member of a highly diverse set of taxa (within the tribe Thelypodieae), described here as the ‘Streptanthoid Complex’ that are adapted to a broad range of environments, yet share a common n = 14 chromosome number and likely arose by a recent radiation. The linkage map consists of 97 polymorphic microsatellite markers, and 40 exon-primed intron-crossing markers based on A. thaliana exon sequences and Brassica ESTs. The map covers 14 linkage groups and has a total length of 1513 cM. Both the patterns of marker segregation and the comparative map indicate that C. amplexicaulis is a diploid organism with a compact genome. All exon-primed intron-crossing markers, and an unexpectedly large number of microsatellite markers (83%), had significant similarity to the A. thaliana genome, facilitating the development of a comparative genome map. As a proof of principle, we used the comparative map to identify candidate genes underlying differences in sepal colour between the two parent taxa. We demonstrate that the genomic tools developed here will be portable throughout the Streptanthoid Complex.
Article
Higher rates of dispersal in one sex than the other are widespread, and often attributed to the genetic advantages of reduced inbreeding. The direction of sex-biased dispersal shows strong phylogenetic conservatism (e.g. males disperse more than females in most mammals, but the reverse is true in most birds). By contrast, our genetic data reveal strong inter-population variation in the relative dispersal rates of two species of sea snakes (Laticauda saintgironsi and L. laticaudata) in the Noumea Lagoon of New Caledonia. Assignment methods using microsatellite data identified parallel variation in sex-specific dispersal in both species: dispersal was female-biased in the north-west of the sampling area (in islands far from the main island), but male-biased in the south-east (in islands closer to the main island). This flexibility may reflect sex differences in diets, with spatial variation in sex-specific resources generating spatial variation in sex-specific dispersal distances.
Article
Exact location and number of glacial refugia still remain unclear for many European cold-blooded terrestrial vertebrates. We performed a fine-scaled multilocus phylogeographic analysis of two Bombina species combining mitochondrial variation of 950 toads from 385 sites and nuclear genes (Rag-1, Ncx-1) from a subset of samples to reconstruct their colonization and contemporary variation patterns. We identified the lowlands northwest of the Black Sea and the Carpathians to be important refugial areas for B. bombina and B. variegata, respectively. This result emphasizes the importance of Central European refugia for ectothermic terrestrial species, far north of the Mediterranean areas regarded as exclusive glacial refugia for the animals. Additional refugia for B. variegata have been located in the southern Apennines and Balkans. In contrast, no evidence for the importance of other east European plains as refugial regions has been found. The distribution of mtDNA and Ncx-1 variation suggests the presence of local refugia near the Black Sea for B. bombina; however, coalescent simulations did not allow to distinguish whether one or two refugia were present in the region. Strong genetic drift apparently accompanied postglacial expansions reducing diversity in the colonization areas. Extended sampling, coupled with the multilocus isolation with migration analysis, revealed a limited and geographically restricted gene flow from the Balkan to Carpathian populations of B. variegata. However, despite proximity of inferred B. bombina and B. variegata refugia, gene exchange between them was not detected.
Article
How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males or are solitary. We genotyped 662 individuals from 54 internodes and analysed parentage of 165 litters. Our results revealed 170 sets of paternal twins/triplets, of which 96 were full-sibs and 74 were half-sibs. We found that males captured roosting with females typically sired more offspring overall than did other males and also showed a greater tendency to monopolize paternity within both litters and roosting groups. In comparison, males that sired fewer full-sibs were assigned more maternal half-sibs. These latter individuals, which included solitary males and those from all-male groups, might gain copulations either via roaming with furtive mating or during visits by females. Indeed, female lesser flat-headed bats store sperm, so could benefit from multiple mating to reduce genetic incompatibilities. At the same time, however, we found no evidence of outbreeding. Finally, relatedness and mtDNA analyses revealed that polygyny also operated within matrilineal kin, suggesting a system that might promote social cohesiveness. Future studies of individual movements will help to determine the extent to which mixed paternities in litters, matrilines and groups are driven by male or female behaviour.
Article
Rodent host dynamics and dispersal are thought to be critical for hantavirus epidemiology as they determine pathogen persistence and transmission within and between host populations. We used landscape genetics to investigate how the population dynamics of the bank vole Myodes glareolus, the host of Puumala hantavirus (PUUV), vary with forest fragmentation and influence PUUV epidemiology. We sampled vole populations within the Ardennes, a French PUUV endemic area. We inferred demographic features such as population size, isolation and migration with regard to landscape configuration. We next analysed the influence of M. glareolus population dynamics on PUUV spatial distribution. Our results revealed that the global metapopulation dynamics of bank voles were strongly shaped by landscape features, including suitable patch size and connectivity. Large effective size in forest might therefore contribute to the higher observed levels of PUUV prevalence. By contrast, populations from hedge networks highly suffered from genetic drift and appeared strongly isolated from all other populations. This might result in high probabilities of local extinction for both M. glareolus and PUUV. Besides, we detected signatures of asymmetric bank vole migration from forests to hedges. These movements were likely to sustain PUUV in fragmented landscapes. In conclusion, our study provided arguments in favour of source-sink dynamics shaping PUUV persistence and spread in heterogeneous, Western European temperate landscapes. It illustrated the potential contribution of landscape genetics to the understanding of the epidemiological processes occurring at this local scale.
Article
The vulnerability of ecologically specialised species to environmental fluctuations has been well documented. However, population genetic structure can influence vulnerability to environmental change and recent studies have indicated that specialised species may have lower genetic diversity and greater population structuring compared to their generalist counterparts. To examine whether there were differences in population genetic structure between a dietary specialist (Chaetodon trifascialis) and a dietary generalist (Chaetodon lunulatus) we compared the demographic history and levels of gene flow of two related coral-feeding butterflyfishes. Using allele frequencies of ≥11 microsatellite loci and >350 bases of mitochondrial control region sequence our analyses of C. trifascialis and C. lunulatus from five locations across the Pacific Ocean revealed contrasting demographic histories and levels of genetic structure. Heterozygosity excess tests, neutrality tests and mismatch distributions were all highly significant in the dietary specialist C. trifascialis (all P < 0.01), suggesting genetic bottlenecks have occurred in all locations. In contrast, we found little evidence of genetic bottlenecks for the dietary generalist C. lunulatus. High gene flow and low genetic structuring was detected among locations for C. trifascialis (amova: R(ST) = 0.0027, P = 0.371; Φ(ST) = 0.068, P < 0.0001). Contrary to our expectations, a greater level of genetic structuring between locations was detected for C. lunulatus (amova: R(ST) = 0.0277, Φ(ST) = 0.166, both P < 0.0001). These results suggest that dietary specialisation may affect demographic history through reductions in population size following resource declines, without affecting population structure through reductions in gene flow in the same way that habitat specialisation appears to. Although C. trifascialis is highly vulnerable to coral loss, the high gene flow detected here suggests populations will be able to recover from local declines through the migration of individuals.
Article
The number of queens per colony and the number of matings per queen are the most important determinants of the genetic structure of ant colonies, and understanding their interrelationship is essential to the study of social evolution. The polygyny-vs.-polyandry hypothesis argues that polygyny and polyandry should be negatively associated because both can result in increased intracolonial genetic variability and have costs. However, evidence for this long-debated hypothesis has been lacking at the intraspecific level. Here, we investigated the colony genetic structure in the Australian bulldog ant Myrmecia brevinoda. The numbers of queens per colony varied from 1 to 6. Nestmate queens within polygynous colonies were on average related (r(qq) = 0.171 ± 0.019), but the overall relatedness between queens and their mates was indistinguishable from zero (r(qm) = 0.037 ± 0.030). Queens were inferred to mate with 1-10 males. A lack of genetic isolation by distance among nests indicated the prevalence of independent colony foundation. In accordance with the polygyny-vs.-polyandry hypothesis, the number of queens per colony was significantly negatively associated with the estimated number of matings (Spearman rank correlation R = -0.490, P = 0.028). This study thus provides the rare intraspecific evidence for the polygyny-vs.-polyandry hypothesis. We suggest that the high costs of multiple matings and the strong effect of multiple mating on intracolonial genetic diversity may be essential to the negative association between polygyny and polyandry and that any attempt to empirically test this hypothesis should place emphasis upon these two key underlying aspects.