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Increased differentiation and reduced gene flow in sex chromosomes relative to autosomes between lineages of the brown creeper Certhia americana


Abstract and Figures

The properties of sex chromosomes, including patterns of inheritance, reduced levels of recombination, and hemizygosity in one of the sexes may result in the faster fixation of new mutations via drift and natural selection. Due to these patterns and processes, the two rules of speciation to describe the genetics of postzygotic isolation, Haldane's rule and the large-X effect, both explicitly include quicker evolution on sex chromosomes relative to autosomes. Because sex-linked mutations may be the first to become fixed in the speciation process, and appear to be due to stronger genetic drift (in birds), we may identify pronounced genetic differentiation in sex chromosomes in taxa experiencing recent speciation and diverging mainly via genetic drift. Here, we use nine sex-linked and 21 autosomal genetic markers to investigate differential divergence and introgression between marker types in Certhia americana. We identified increased levels of genetic differentiation and reduced levels of gene flow on sex chromosomes relative to autosomes. This pattern is similar to those observed in other recently-divergent avian species, providing another case study of the earlier role of sex chromosomes in divergence, relative to autosomes. Additionally, we identify three markers that may be under selection between Certhia americana lineages.
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Increased differentiation and reduced gene flow in sex
chromosomes relative to autosomes between lineages
of the brown creeper Certhia americana
Joseph D. Manthey and Garth M. Spellman
J. D. Manthey (, Biodiversity Inst. and Dept of Ecology and Evolutionary Biology, Univ. of Kansas, Lawrence,
KS 66045, USA. – JDM and G. M. Spellman, Center for the Conservation of Biological Resources, Dept of Biology, Black Hills State Univ.,
Spearfish, SD 57799, USA.
e properties of sex chromosomes, including patterns of inheritance, reduced levels of recombination, and hemizygosity
in one of the sexes may result in the faster fixation of new mutations via drift and natural selection. Due to these patterns
and processes, the two rules of speciation to describe the genetics of postzygotic isolation, Haldane’s rule and the
large-X effect, both explicitly include quicker evolution on sex chromosomes relative to autosomes. Because sex-linked
mutations may be the first to become fixed in the speciation process, and appear to be due to stronger genetic drift (in
birds), we may identify pronounced genetic differentiation in sex chromosomes in taxa experiencing recent speciation
and diverging mainly via genetic drift. Here, we use nine sex-linked and 21 autosomal genetic markers to investigate
differential divergence and introgression between marker types in Certhia americana. We identified increased levels
of genetic differentiation and reduced levels of gene flow on sex chromosomes relative to autosomes. is pattern is
similar to those observed in other recently-divergent avian species, providing another case study of the earlier role of sex
chromosomes in divergence, relative to autosomes. Additionally, we identify three markers that may be under selection
between Certhia americana lineages.
Birds, snakes, butterflies, and some fishes and lizards exhibit
female heterogamety and Z–W sex determination. Certain
properties of sex chromosomes, including patterns of inheri-
tance, reduced levels of recombination, and hemizygosity in
one of the sexes (Vicoso and Charlesworth 2006) can result
in the faster fixation of new mutations via drift and natural
selection. ese properties have led to the explicit inclusion
of sex chromosomes in the two rules of speciation used to
characterize the genetics of postzygotic isolation: Haldane’s
rule and the large-X effect (Coyne and Orr 1989).
Haldane’s rule states that hybrid incompatibility is more
pronounced in the heterogametic sex due to expression of
hemizygous (Z-linked) alleles, whether recessive or domi-
nant (Haldane 1922). ree main hypotheses have been pro-
posed to explain Haldane’s rule, including the faster-male
hypothesis, dominance, and the fast-Z. e faster-male
hypothesis suggests evolution on sex chromosomes is quick-
ened due to sexual selection on males, which would reduce
the effective population size of Z-chromosomes (NEZ) rela-
tive to the effective population size of autosomes (NEA),
thereby increasing the effects of genetic drift (Wu and Davis
1993); the faster-male hypothesis could be exacerbated fur-
ther by skew in operational sex ratio, leading to larger vari-
ance in differences between NEZ and NEA. e dominance
hypothesis of Haldane’s rule states that mutations involved
in reduced hybrid fitness are on average recessive; therefore
the negative effects of these mutations is more pronounced if
they are located on sex chromosomes, where they would be
expressed in the heterogametic sex (Turelli and Orr 1995).
Finally, the fast-Z effect suggests that sex chromosomes may
exhibit faster rates of adaptive change compared to auto-
somes (Charlesworth et al. 1987), although these effects
may be caused in part by the faster-male or dominance
hypotheses, as well as vary in effect between species due to
differences in effective population size (Mank et al. 2010a).
e second rule of speciation is the large-X, or in the case of
birds, the large-Z effect, which states that mutations on the
Z chromosome have a relatively large effect on hybrid fitness
compared to similar mutations on autosomes (Charlesworth
et al. 1987, Coyne and Orr 1989).
Because the two rules of speciation explicitly tie sex
chromosomes to speciation, the Z chromosome often may
be responsible for the development of pre- (e.g. cellular
incompatibilities) or postzygotic (e.g. male plumage char-
acteristics; Mank et al. 2010b) reproductive isolation in
recently diverged species. Several recent studies of contact
zones between bird species (Sæther et al. 2007, Carling and
Brumfield 2009, Storchova et al. 2010, Backström and
Väli 2011, Elgvin et al. 2011) have shown reduced levels
of introgression between species in Z-linked markers
Journal of Avian Biology 44: 001–008, 2013
doi: 10.1111/j.1600-048X.2013.00233.x
© 2013 e Authors. Journal of Avian Biology © 2013 Nordic Society Oikos
Subject Editor: Staffan Bensch. Accepted 3 September 2013
compared to autosomal markers, supporting the strong role
of sex-linked mutations in speciation. Additionally, a study
by Mank et al. (2010b) investigated the fast-Z effect using
the genome drafts of Taeniopygia guttata and Gallus gallus.
ey found a lack of positive selection, and hypothesized
that the fast-Z may be predominantly due to increased
effects of genetic drift, potentially from sexual selection in
males reducing NEZ (i.e. partially from the faster-male
Because sex-linked mutations may be the first to become
fixed in the evolution of reproductive isolation, and appear
to be due to increased efficacy of genetic drift in birds (Mank
et al. 2010b), Z-linked markers may be relatively strongly
differentiated in taxa exhibiting recent speciation and diverg-
ing mainly under genetic drift. e brown creeper Certhia
americana, a widespread North American avian taxon, is cur-
rently considered a single species (AOU 1983); however,
recent phylogeographic studies (Manthey et al. 2011a, b)
suggest C. americana is two species. Mitochondrial and
nuclear DNA identified a basal split between northern and
southern populations at approximately 32°N latitude. is
split occurred recently (~ 1.50 million yr ago), with diver-
gence between populations caused by isolation (genetic drift)
and lack of gene flow (Manthey et al. 2011a, b).
Here, using nine sex-linked and 21 autosomal markers,
we measure divergence and fixation between Certhia lin-
eages and determine if genetic markers are evolving under
neutral processes or via selection. Although we cannot test
specific processes described above relating to fitness and
hybrid incompatibilities, we aim to examine the relative
effects of sex chromosomes on differentiation between
Certhia lineages. Using these data, we examine the follow-
ing hypotheses: (H01) Differentiation between lineages will
be greater in sex-linked markers than autosomal markers;
(H02) Sex-linked markers will exhibit relatively less gene
flow between lineages.
Sampling and laboratory procedures
Tissue samples of 16 brown creeper individuals were obtained
from two populations, representing the basal lineages identi-
fied in phylogeographic studies (Manthey et al. 2011a, b).
ese samples were from LaPlata County, CO, USA (n 8)
and the state of Jalisco in Mexico (n 8). One sample of the
Eurasian treecreeper Certhia familiaris was used as an out-
group taxon. We attempted to minimize any effects of sam-
ple size on estimates of polymorphism and divergence by
sampling mainly males (only one female included in this
study). Because one female was included, all analyses
included 31 alleles for Z-linked markers and 32 alleles for
autosomal markers.
Total genomic DNA was previously extracted for earlier
studies. e sequences of 21 autosomal loci were obtained
from Manthey et al. (2011b), which included anonymous
loci (developed in that study) and introns (developed by
Backström et al. 2008). An additional nine Z-linked introns
were obtained using polymerase chain reaction (PCR) ampli-
fication with previously designed primers (Backström et al.
2006, 2010, Kimball et al. 2009). PCR amplification of all
sequences was carried out in 15 ml reactions and included an
initial denaturation period of 10 min at 95°C, with 40
subsequent cycles of 95°C for 30 s, TA for 45 s, and 72°C for
1 min; annealing temperature varied with loci and samples
from 55–61°C. PCR products were purified and sequenced
using 10 ml ABI BigDye sequencing reactions. Sequencing
reactions were purified using a standard ethanol precipita-
tion clean-up followed by sequencing on an ABI 3130
Genetic Analyzer.
Phased and trimmed haplotype sequences were taken
directly from Manthey et al. (2011b) for the autosomal
sequences, which were previously checked (and trimmed if
necessary) for recombination. Newly sequenced loci were
processed using the following methodology. Sequences were
automatically aligned and manually checked and edited
using Sequencher 4.8 (GeneCodes). On introns, any partial
exon sequence was removed prior to analyses. Haplotypes
were inferred using PHASE (Stephens et al. 2001, Stephens
and Donelly 2003), with an output threshold of 0.7, as
implemented in DnaSP (Librado and Rozas 2009). Using
RDP3, and seven inclusive tests in the program (Smith 1992,
Padidam et al. 1999, Gibbs et al. 2000, Martin and Rybicki
2000, Posada and Crandall 2001, Martin et al. 2005, Heath
et al. 2006, Boni et al. 2007), we checked for recombination.
Using these tests, recombination was not detected in any of
the Z-linked loci.
Levels of variation, neutrality and selection
Measures of genetic diversity (polymorphic sites and nucle-
otide diversity (p)) and neutrality statistics (Tajima’s D;
(Tajima 1989) and Fu and Li’s D* (Fu and Li 1993)) were
estimated using DnaSP ver. 5 (Librado and Rozas 2009).
Significance of neutrality indices was inferred via 1000
bootstrap replicates implemented directly in DnaSP. Taji-
ma’s D uses the number of segregating sites and nucleotide
diversity in a genetic marker to identify an excess or lack of
polymorphisms, signifying population size changes or
selection. Similarly, Fu and Li’s D* investigates polymor-
phism frequencies, although focusing on singletons, to
identify purifying selection or recent selective sweeps.
To identify loci under selection, we used two tests: 1)
the Hudson–Kreitman–Aguade (HKA) test (Hudson et al.
1987, implemented online at: http://genfaculty.rutgers.
edu/hey/software#HKA ), and 2) a Bayesian method,
implemented in BAYESFST (Beaumont and Balding
2004). HKA compares ratios of polymorphisms to diver-
gence levels to identify signals (or lack thereof) of selection
in an entire dataset. We compared the two lineages of
C. americana, performing the test using 10 000 coalescent
simulations for three datasets: 1) all loci together,
2) Z-linked loci, and 3) autosomal loci. BAYESFST identi-
fies individual loci that exhibit a signal of selection by
implementing an MCMC to estimate locus, population,
and population-by-locus interaction effects. Using default
settings, we ran five iterations of BAYESFST to ensure
replicative results, again with three datasets (as with
the HKA test). We applied a 5% significance level to the
tests, which corresponds to an approximate transformed
p-value of 2.94; low outliers suggest loci evolving under
balancing selection while high outliers suggest loci evolving
under diversifying selection.
Investigation of population structure and gene flow
We investigated population structure and genetic-structure
variation between autosomal and sex-linked markers using
several methods: 1) private, shared and fixed polymor-
phisms, 2) summary statistics, including the fixation index
(FST; Hudson et al. 1992) and relative node depth (RND;
Feder et al. 2005), and 3) a measure of genetic differentia-
tion and population sorting that uses phylogenies, the gene-
alogical sorting index (GSI; Cummings et al. 2008). e
RND is measured as the average pairwise divergence (Dxy;
Nei 1987) between lineages divided by Dxy between all
C. americana samples and the outgroup (C. familiaris).
e RND was used to identify ‘fast’ evolution between
C. americana lineages relative to the outgroup. e GSI is a
normalized statistic that quantifies exclusive ancestry of
populations in gene trees. Input for calculating the
GSI are gene trees for each locus. erefore, TOPALi ver.
2.5 (Milne et al. 2009), using a PhyML analysis (Guindon
and Gascuel 2003), was used to construct maximum likeli-
hood phylogenies for each locus. GSI values range from 0
(complete mixing of populations in the gene tree) to 1
(monophyly) with significance assessed by comparing
observed values to values obtained from 10 000 permuta-
tions of the individuals assigned to each gene trees tips.
Because the GSI is a standardized statistic, the value of GSI
for all loci can be combined to produce an ensemble GSI,
which measures the structure of populations in an entire
To investigate gene flow between lineages we used a
coalescent method implemented in the Isolation with Migra-
tion (IMa) software (Hey and Nielsen 2007) using separate
datasets for autosomal and Z-linked loci. Trial runs were
used to identify appropriate priors for the IMa model;
following trial runs, we ran IMa for a burn-in period of
500 000 steps followed by 100 million iterations ( 100
effective sample size for each parameter). We performed
three runs of IMa with identical priors and different starting
seeds to assess convergence. Additionally, we used log-likeli-
hood ratio tests of nested models implemented in IMa to
determine if models identifying no or asymmetrical migra-
tion explained the data as well as the full model. Nested
models were ranked using Akaike’s information criterion
(AIC; Carstens et al. 2009).
In total, 3271 base pairs from nine Z-linked loci were
sequenced for 16 brown creeper samples and supplemented
with 5063 base pairs from 21 autosomal loci from Manthey
et al. (2011b). One sample from the data matrix, from the
locus MUSK, could not be sequenced. For all Z-linked loci,
except BRM15, one sample of Certhia familiaris was
sequenced. Few (3/9) Z-linked loci shared any haplotypes
between populations, while the majority (15/21) of auto-
somal loci shared haplotypes between populations. DNA
sequences obtained in this study were deposited in GenBank
under accession numbers KF570392 – KF570652. Sequences
shorter than 200 base pairs are provided in the Supplemen-
tary material Appendix 1 because GenBank currently does
not accept sequences of this length.
Genetic diversity, neutrality and selection
Estimates of genetic diversity are shown in Table 1 and
Fig. 1. In general, the southern population exhibited greater
genetic diversity. In the northern population (southern
population), nucleotide diversity ranges from 0–0.67%
(0.03–0.88%) and 0–1.57% (0–1.99%) in Z-linked and
autosomal loci, respectively. Variance in nucleotide diversity
was significantly higher in autosomal loci for the northern
population (Levene’s test; p 0.028) but not significantly
different between marker types in the southern population
(p 0.235). None of the loci deviated from neutrality
using both Tajima’s D and Fu and Li’s D* (Table 1).
e HKA test did not reject evolution under the neutral
model for the Z-linked (p 0.595), the autosomal
(p 0.969) or the combined (p 0.973) datasets. BAYES-
FST results identified seven outlier loci (Fig. 2) with the full
dataset (all loci). ree loci (MUSK, Ca34, and Ca65) are
suggestive of disruptive selection and four (MADH2, 00895,
13093, and Ca9) of balancing selection. BAYESFST results
for the autosomal and Z-linked datasets identified the same
outliers (results not shown) with the exception of MUSK,
which was not an outlier in the dataset with only Z-linked
Genetic structure and gene flow
Z-linked markers exhibit a smaller level of shared polymor-
phisms between populations, while having more than
double the amount of fixed polymorphisms (Fig. 1, Table 1).
e mean FST for Z-linked loci is higher (Mann–Whitney
U-test; p 0.014) than autosomal loci (Table 1, Fig. 3).
Autosomal Loci
Z-linked loci
0 0.008 0.016
Proportion of base pairs polymorphic
Figure 1. Rates of polymorphisms in autosomal and Z-linked
markers, represented as proportion of total number of base pairs
that are polymorphic. Private polymorphisms (North and South),
polymorphisms shared between lineages (Shared) and polymor-
phisms fixed between lineages (Fixed).
In this study, we identified increased levels of genetic dif-
ferentiation between lineages of C. americana on sex chro-
mosomes relative to autosomes (Fig. 1, Table 1), supporting
H01 (differentiation between lineages will be greater in
sex-linked markers than autosomal markers). e observed
levels of fixed differences on sex chromosomes (2.05 the
autosomal level) are higher than what would be expected
under neutral evolution (~ 1.33). e ratio drops, but is still
higher (1.56 the autosomal level) than what would be
expected, when loci putatively evolving under selection are
removed. ese deviations from strict neutral evolution
could be due to sexual selection in males, causing deviations
in NEZ (Wu and Davis 1993), specific population size effects
in birds (Mank et al. 2010a), or higher variance in male
reproductive success (Barker et al. 2008), leading to a
larger signal of faster-Z differentiation between lineages.
Alternatively, the levels observed here might be within the
expected variance of fixed differences given the number of
base pairs sampled.
Additionally, we find reduced gene flow between
lineages on sex chromosomes (Table 2), supporting H02
(sex-linked markers will exhibit relatively less gene flow
between lineages). ese estimates are limited in inferring
between pre-divergence genetic structure and post-divergence
gene flow (Becquet and Przeworkski 2009); however, either
interpretation (i.e. high pre-divergence structure or low post-
divergence gene flow on sex chromosomes) lends weight to
the hypothesis of the importance of sex chromosomes in the
speciation process in Certhia americana. Sampling individu-
als from a single population for each lineage introduces a
potential bias in parameter estimation of gene flow (includ-
ing potential biases in effective population size estimation);
however, this sampling regime limits the effects of genetic
structure within each lineage in inducing further biases
in IMa, as both the northern and southern lineages of
C. americana have strong population structure (Wahlund
1928, Manthey et al. 2011a, b).
Autosomal FST comparisons have a greater range (0.000–
0.941) than Z-linked FST comparisons (0.4438–0.9636),
but do not have a significantly greater variance (p 0.238).
Interestingly, in Z-linked loci, nucleotide diversity of the
southern population was negatively correlated with FST sta-
tistics (r –0.770, p 0.015) while northern nucleotide
diversity was not (p 0.585). In autosomal loci, FST com-
parisons are not correlated with nucleotide diversity in the
northern (p 0.071) or the southern lineage (p 0.089),
but nucleotide diversity between lineages is correlated
(p 0.001). While these properties may be biologically
meaningful (e.g. different patterns of genetic diversity rela-
tionships with FST in Z-linked markers between lineages),
genetic diversity patterns between populations can limit
upper bounds of FST estimates (Jakobsson et al. 2013) which
may have led to the observed pattern.
Estimates of RND and Dxy (Table 1, Fig. 3) were, on
average, higher in Z-linked loci, although it was not statisti-
cally significant (Mann–Whitney U-test; Dxy p-value 0.330;
RND p-value 0.647). Ensemble GSI statistics were
approximately the same for each population (Table 1). GSI
statistics were significant for a majority of loci in both the
southern (8/9 Z-linked and 15/20 autosomal) and the north-
ern (8/9 Z-linked and 9/20 autosomal) populations. Many
of the loci show nested monophyly of one population (5/9
Z-linked and 7/21 autosomal) with the other paraphyletic
(one population’s GSI 1.00 and the other’s GSI 0.88).
Gene flow estimates from coalescent-based analyses
(2Nm), as implemented in IMa, were lower in Z-linked
loci than autosomal loci (Table 2). Analyses of nested mod-
els identified models with reduced number of parameters
that could explain the data as well as the full model (Sup-
pementary material Appendix 1, Table A1, A2). However,
when using the AIC, the full model was best for the auto-
somal dataset and a model with zero migration north to
south was best for the Z-linked model. Although we
detected non-zero gene flow in coalescent-based estimates,
it is not substantial enough (2Nm 2) to counteract the
effects of genetic drift (Wright 1931, Slatkin 1987).
–5 –3 –1 1357
Transformed p-value; logit(2|P-0.5|)
Figure 2. Results from the BAYESFST analysis of all loci. e estimates of FST plotted against empirical p-values for each locus. e
vertical bar shows the 0.05 significance level (~ 2.94 transformed p-value) used for identifying outlier loci. In analyses with autosomal or
Z-linked specific markers, results were the same as the full dataset with the exception of MUSK (denoted with an *) not being recognized
as an outlier.
0.0 0.2 0.4 0.6 0.8 1.0
Figure 3. FST values between lineages for each marker. e top nine markers are Z-linked and the bottom 21 are autosomal.
Lines through values indicate averages for each dataset separately.
Patterns of reduced gene flow between lineages and
increased genetic differentiation between lineages in sex
chromosomes are similar to patterns observed in other
closely related avian species, including Ficedula flycatchers
(Sætre et al. 2003, Borge et al. 2005), Luscinia nightin-
gales (Storchova et al. 2010), Passer sparrows (Elgvin et al.
2011) and Passerina buntings (Carling and Brumfield
2008, 2009). Alternatively, other avian species (often with
low overall genetic differentiation) have shown greater
intraspecific Z-linked gene flow (Dallimer et al. 2002, Li
and Merila 2010). ese patterns may suggest that
increased levels of differentiation on Z-linked markers and
reduced introgression only occur following significant
divergence in allopatry (as opposed to within species
between localities). On average, RND indicates the north-
ern and southern C. americana lineages are nearly as diver-
gent as C. americana is to its sister-species (C. familiaris),
providing further support to previous literature (Manthey
et al. 2011a, b) suggesting significant divergence in allopa-
try between C. americana lineages.
Higher levels of differentiation and reduced levels of
gene flow on sex chromosomes also could be attributed to
female biased dispersal. Multiple lines of evidence suggest
biased dispersal is not the cause of this pattern. While no
studies have investigated natal philopatry in C. americana,
studies in C. familiaris show patterns of site tenacity follow-
ing establishment of territories (Cramp and Perrins 1993,
Peach et al. 1995) while young birds will disperse at least one
kilometer (Suorsa et al. 2003). ough Certhia species may
have short natal dispersal distances, they are likely inconse-
quential; research on C. americana song in California dem-
onstrates the formation of local dialects in populations less
than 50 km apart (Baptista and Krebs 2000). Finally, coales-
cent estimates of gene flow (all estimates of 2Nm 2)
between the northern and southern clades of C. americana
(this study and Manthey et al. 2011b) indicate gene
flow, including male- or female-biased gene flow, was incon-
sequential in the evolutionary history of these lineages.
In general, the overall dataset did not deviate from
neutrality (HKA test, neutrality statistics; Table 1), however,
Table 1. Per locus statistics of polymorphism neutrality, and divergence. Statistics include: base pairs of marker (BP), nucleotide
diversity ( 100) in the north (p N) and south (p S), number of polymorphisms in the northern (N) and southern (S) lineages, number of
shared polymorphisms (PS), number of fixed polymorphisms (PF), Tajima’s D (TD), Fu and Li’s D (FLD), FST, relative node depth (RND), and
genealogical sorting index of the southern (GSI S) and northern lineage (GSI N). Significance (p 0.05) of neutrality indices and sample-
size corrected significance (p 0.05) of GSI indicated by an asterisk (*).
MADH2 (Z) 482 0.667 0.535 10 10 5 0 0.24 20.62 0.53 20.73 0.4438 0.636 0.88*0.43*
PTCH6 (Z) 540 0.235 0.101 3 1 0 3 1.08 1.50 1.04 0.70 0.8120 0.743 1.00*0.88*
ALDOB3 (Z) 137 0 0.875 0 3 0 0 0.83 1.06 0.5079 0.759 0.03 0.76*
MUSK (Z) 349 0.108 0.044 3 1 0 7 21.70 21.15 22.20 21.37 0.9636 1.614 0.88*1.00*
GPBP1 (Z) 212 0.248 0.288 1 2 0 2 1.47 20.02 0.69 20.48 0.8468 1.883 0.88*1.00*
PPWD1 (Z) 423 0.238 0.515 6 7 0 0 20.58 20.18 0.91 20.75 0.4516 0.628 0.88*1.00*
IQGAP2 (Z) 395 0.095 0.034 3 1 0 3 21.70 21.16 22.20 21.43 0.9384 1.008 0.88*1.00*
BRM15 (Z) 290 0 0.795 0 8 0 1 20.23 0.33 0.5061 0.88*1.00*
24105 (Z) 443 0.102 0.194 2 4 0 0 20.65 20.97 20.50 20.60 0.5128 0.175 0.67*0.25
13093 (3) 322 1.571 1.991 16 14 11 0 20.06 1.28 0.41 1.23 0.0570 1.311 0.10 0.33
00895 (28) 218 0.665 0.887 3 7 3 0 1.75 20.29 1.04 20.44 0.0626 1.375 0.33 0.33
02108 (15) 194 1.349 0.851 6 4 2 0 1.53 1.15 1.27 1.14 0.1466 0.527 0.45*0.33
22528 (2) 265 0.579 0.333 5 3 0 0 0.06 20.07 0.46 1.04 0.1944 0.480 0.45*0.38
04550 (15) 89 0.539 0.627 1 1 1 0 1.03 1.53 0.69 0.69 0.0083 0.841 0.45*0.33
Ca4 (1A) 266 0.219 0 2 0 0 0 20.08 20.50 0.2222 0.316 0.77*0.03
Ca8 (21) 172 0.000
Ca9 (20) 274 1.183 1.128 9 10 7 0 0.72 0.10 0.91 20.35 0.0137 0.988 0.52*0.18
Ca10 (4A) 258 0.266 0.217 3 2 0 2 20.71 20.19 20.04 0.91 0.8125 0.906 0.88*1.00*
Ca13 (6) 266 0.595 0.746 4 9 1 0 0.98 20.99 1.14 21.01 0.4425 0.826 0.59*0.88*
Ca14 (3) 264 0.325 0.533 3 5 1 2 20.15 20.22 20.04 21.05 0.6832 1.300 1.00*0.88*
Ca15 (2) 227 0.737 0.671 5 6 2 0 0.19 20.68 0.46 20.05 0.1680 0.527 0.38 0.38
Ca21 (1) 216 0 0.847 0 5 0 2 0.19 0.46 0.6141 0.230 0.88*1.00*
Ca29 (1A) 189 0.401 0.366 2 2 1 0 0.66 0.91 0.91 0.91 0.0626 0.217 0.45*0.18
Ca34 (8) 222 0.180 0 1 0 0 1 0.65 0.69 0.8857 1.00*0.88*
Ca47 (24) 286 0.398 0.702 3 8 3 0 0.74 20.61 1.04 20.23 0.1126 0.807 0.14 0.33
Ca50 (12) 282 0 0.165 0 1 0 0 1.03 0.69 0.2666 0.086 0.88*1.00*
Ca51 (19) 290 0 0.129 0 3 0 0 21.70 22.20 0.0000 2.031 0.00 0.27
Ca57 (1) 256 0.358 0.140 2 2 0 3 1.33 21.04 0.91 20.50 0.8477 0.912 0.88*1.00*
Ca58 (5) 246 0.262 0.458 2 4 0 0 0.84 20.25 0.72 20.63 0.4426 0.413 0.68*0.59*
Ca65 (3) 261 0.048 0.048 1 1 0 2 21.16 21.16 21.45 21.45 0.9411 2.000 1.00*0.88*
Z-linked 3271 0.188 0.376 28 37 5 16 0.6648 0.931 0.77*0.81*
Autosomal 5063 0.461 0.516 68 87 32 12 0.3326 0.804 0.58*0.55*
Overall 8334 0.379 0.474 96 124 37 28 0.4323 0.841 0.64*0.63*
Table 2. Coalescent-based (from IMa) estimates of gene flow (2Nm)
from north to south (southward) and south to north (northward),
with associated 95% confidence intervals. Three replicate runs were
performed for sex-linked (Z) and autosomal (A) loci with different
starting seeds.
95% CI Northward
95% CI
Z1 0.036 0.004–0.750 0.036 0.005–0.446
Z2 0.035 0.004–0.753 0.038 0.006–0.447
Z3 0.037 0.004–0.748 0.037 0.006–0.446
A1 0.230 0.022–1.221 0.385 0.114–1.452
A2 0.230 0.021–1.221 0.386 0.115–1.456
A3 0.229 0.021–1.219 0.383 0.115–1.461
in BayesFST analyses, three markers were identified as
potentially evolving under disruptive or directional selec-
tion (Fig. 2). Of these markers, more mapped to autosomes
than sex chromosomes, suggesting no clear trend in pat-
terns of selection based on marker type. ese results could
be caused by differential levels of gene flow between mark-
ers or marker-types, potentially causing positive results in
the BayesFST test; these caveats suggest we should inter-
pret these results with caution, as positive selection, or
genetic drift with reduced gene flow, may be driving the
observed patterns of sequence divergence in these loci.
When differentiation is investigated in concert with RND
(Table 1), the majority of Z-linked and autosomal markers
is not diverging between lineages faster than expected com-
pared to outgroup data, although two of the outliers in the
BAYESFST analysis (Ca65 and MUSK) had FST values
0.9 and RND values 1.6 (in Ca34 the outgroup
could not be amplified). ese combined patterns suggest
Ca65 and MUSK are good candidates for further investiga-
tion of selection.
Two lines of evidence suggest the selection patterns in the
data are driven by directional selection in the southern
lineage rather than disruptive selection between lineages.
First, we identified a negative correlation between differen-
tiation and genetic diversity in the southern lineage and no
relationship between differentiation and genetic diversity in
the northern lineage. Under strict neutral evolution, it is
expected that interspecific differentiation will be positively
correlated with intraspecific genetic diversity (Kimura 1983,
Li and Graur 2006). Second, in sex-linked markers, seven
loci show patterns of nested monophyly based on the GSI
(Table 1). Six of these indicate the southern lineage is nested
Carling, M. D. and Brumfield, R. T. 2009. Speciation in Passerina
buntings: introgression patterns of sex-linked loci identify a
candidate gene region for reproductive isolation. – Mol. Ecol.
18: 834–847.
Carstens, B. C., Stoute, H. N. and Reid, N. M. 2009. An
information-theoretical approach to phylogeography. – Mol.
Ecol. 18: 4270–4282.
Charlesworth, B., Coyne, J. A. and Barton, N. H. 1987. e rela-
tive rates of evolution of sex chromosomes and autosomes.
– Am. Nat. 130: 113–146.
Coyne, J. A. and Orr, H. A. 1989. Two rules of speciation. – In:
Otte, D. and Endler, J. ( eds), Speciation and its consequences,
Sinauer, pp. 180–207.
Cramp, S. and Perrins, C. M. 1993. e birds of the Western
Palearctic, Vol. 7: flycatchers to shrikes. Oxford Univ.
Cummings, M. P., Neel, M. C. and Shaw, K. L. 2008. A
genealogical approach to quantifying lineage divergence.
– Evolution 62: 2411–2422.
Dallimer, M., Blackburn, C., Jones, P. J. and Pemberton, J. M.
2002. Genetic evidence for male biased dispersal in the
red-billed quelea Quelea quelea. – Mol. Ecol. 11: 529–533.
Elgvin, T. O., Hermansen, J. S., Fuarczyk, A., Bonnet, T., Borge,
T., Sæther, S. A., Voje, K. L. and Sætre, G.-P. 2011. Hybrid
speciation in sparrows II: a role for sex chromosomes? – Mol.
Ecol. 20: 3823–3937.
Feder, J. L., Xie, X. F., Rull, J., Velez, S., Forbes, A., Leung, B.,
Dambroski, H., Filchak, K. E. and Aluja, M. 2005. Mayr,
Dobzhansky, and Bush and the complexities of sympatric
speciation in Rhagoletis. – Proc. Natl Acad. Sci. USA 102:
Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of
mutations. – Genetics 133: 693–709.
Gibbs, M. J., Armstrong, J. S. and Gibbs, A. J. 2000. Sister-
scanning: a Monte Carlo procedure for assessing signals in
recombinant sequences. – Bioinformatics 16: 573–582.
Guindon, S. and Gascuel, O. 2003. A simple, fast, and accurate
algorithm to estimate large phylogenies by maximum likeli-
hood. – Syst. Biol. 52: 696–704.
Haldane, J. B. S. 1922. Sex ratio and unisexual sterility in hybrid
animals. – Genetics 12: 101–109.
Heath, L., van der Walt, E., Varsani, A. and Martin, D. P. 2006.
Recombination patterns in aphthoviruses mirror those
found in other picornaviruses. – J. Virol. 80: 11827–11832.
Hey, J. and Nielsen, R. 2007. Integration within the Felsenstein
equation for improved Markov chain Monte Carlo methods
in population genetics. – Proc. Natl Acad. Sci. USA 104:
Hudson, R. R., Kreitman, M. and Aguade, M. 1987. A test
of neutral molecular evolution based on nucleotide data.
– Genetics 116: 153–159.
Hudson, R. R., Slatkin, M. and Maddison, W. P. 1992. Estimation
of levels of gene flow from DNA sequence data. – Genetics
132: 583–589.
Jakobsson, M., Edge, M. D. and Rosenberg, N. A. 2013. e
relationship between FST and the frequency of the most
frequent allele. – Genetics 193: 515–528.
Kimball, T. R., Braun, E. L., Barker, F. K., Bowie, R. C. K.
et al. 2009. A well-tested set of primers to amplify regions
across the avian genome. Mol. Phylogenet. Evol. 50:
Kimura, M. 1983. e neutral theory of molecular evolution.
– Cambridge Univ. Press.
Li, M. H. and Merila, J. 2010. Genetic evidence for male-biased
dispersal in the Siberian jay (Perisoreus infaustus) based on
autosomal and Z-chromosomal markers. – Mol. Ecol. 19:
Li, W. and Graur, D. 2006. Molecular evolution. – Sinauer.
within the north, indicating a trend toward which lineage is
evolving quicker (although not statistically significant in a
binomial test; p 0.125). Conversely, in autosomal loci,
there is no clear trend toward which lineage shows signals of
nested monophyly (three of seven in south; binomial test
p 1). ese two patterns suggest that sex-linked loci are
creating a signature of selective sweeps in the southern lin-
eage, causing reduced genetic diversity in loci with stronger
differentiation between lineages. Alternatively, variation in
effective population size, and subsequent drift, could also
be causing the observed patterns. A future detailed investi-
gation of introgression patterns would be insightful as to
which of these scenarios is most likely accurate.
Acknowledgements – We would like to thank the state, provincial,
and federal agencies and wildlife officers for their cooperation
and help obtaining permits that contributed to this research.
is project was funded in part by the Nathaniel R. Whitney Jr
Memorial Research Grant from the South Dakota Ornithologists’
Union and the National Science Foundation (NSF DEB
AOU 1983. Check-list of North American birds. – Am. Ornithol.
Union, Washington, DC.
Backström, N. and Väli, Ü. 2011. Sex- and species-biased
gene flow in a spotted eagle hybrid zone. – BMC Evol. Biol.
11: 100.
Backström, N., Brandström, M., Gustafsson, L., Qvarnström, A.,
Cheng, H. and Ellegren, H. 2006. Genetic mapping in a
natural population of collared flycatchers (Ficedula albicollis):
conserved synteny but gene order rearrangements on the
avian Z chromosome. – Genetics 174: 377–386.
Backström, N., Fagerberg, S. and Ellegren, H. 2008. Genomics of
natural bird populations: a gene-based set of reference
markers evenly spread across the avian genome. – Mol. Ecol.
17: 964–980.
Backström, N., Lindell, J., Zhang, Y., Palkopoulou, E., Qvarn-
ström, A., Sætre, G. P. and Ellegren, H. 2010. A high-
density scan of the Z chromosome in Ficedula flycatchers
reveals candidate loci for diversifying selection. Evolution
64: 3461–3475.
Baptista, L. F. and Krebs, R. 2000. Vocalization and relationships
of brown creepers Certhia americana: a taxonomic mystery.
– Ibis 142: 457–465.
Beaumont, M. A. and Balding, D. J. 2004. Identifying adaptive
genetic divergence among populations from genome scans.
– Mol. Ecol. 13: 969–980.
Becquet, C. and Przeworski, M. 2009. Learning about modes of
speciation by computational approaches. Evolution 63:
Boni, M. F., Posada, D. and Feldman, M. W. 2007. An exact
nonparametric method for inferring mosaic structure in
sequence triplets. – Genetics 176: 1035–1047.
Borge, T., Webster, M., Andersson, G. and Sætre, G.-P. 2005.
Contrasting patterns of polymorphism and divergence on
the Z chromosome and autosomes in two Ficedula flycatcher
species. – Genetics 171: 1861–1873.
Carling, M. D. and Brumfield, R. T. 2008. Haldane’s rule in an
avian system: using cline theory and divergence population
genetics to test for differential introgression of mitochondrial,
autosomal, and sex-linked loci across the Passerina bunting
hybrid zone. – Evolution 62: 2600–2615.
S., Kral, M., Hjernquist, M. B., Gustafsson, L., Traff, J.
and Qvarnström, A. 2007. Sex chromosome-linked species
recognition and evolution of reproductive isolation in flycatch-
ers. – Science 318: 95–97.
Sætre, G. P., Borge, T., Lindroos, K., Haavie, J., Sheldon, B. C.,
Primmer, C. and Syvanen, A. C. 2003. Sex chromosome
evolution and speciation in Ficedula flycatchers. – Proc. R. Soc.
B 270: 53–59.
Slatkin, M. 1987. Gene flow and the geographic structure of
natural populations. – Science 236: 787–792.
Smith, J. M. 1992. Analyzing the mosaic structure of genes.
– J. Mol. Evol. 34: 126–129.
Stephens, M. and Donnelly, P. 2003. A comparison of Bayesian
methods for haplotype reconstruction from population
genotype data. – Am. J. Hum. Genet. 73: 1162–1169.
Stephens, M., Smith, N. and Donnelly, P. 2001. A new statistical
method for haplotype reconstruction from population data.
– Am. J. Hum. Genet. 68: 978–989.
Storchova, R., Reif, J. and Nachman, M. W. 2010. Female
heterogamety and speciation: reduced introgression of the Z
chromosome between two species of nightingales. – Evolution
64: 456–471.
Suorsa, P., Helle, H., Huhta, E., Jantti, A., Nikula, A. and
Hakkarainen, H. 2003. Forest fragmentation is associated
with primary brood sex ratio in the treecreeper (Certhia
familiaris). – Proc. R. Soc. B 270: 2215–2222.
Tajima, F. 1989. Statistical methods to test for nucleotide
mutation hypothesis by DNA polymorphism. – Genetics 123:
Turelli, M. and Orr, H. A. 1995. e dominance theory of
Haldane’s rule. – Genetics 140: 389–402.
Vicoso, B. and Charlesworth, B. 2006. Evolution on the X
chromosome: unusual patterns and processes. – Nat. Rev.
Genet. 7: 645–653.
Wahlund, S. 1928. Zusammensetzung von Population und
Korrelationserscheinung vom Standpunkt der Vererbungslehre
aus betrachtet. – Hereditas 11: 65–106.
Wright, S. 1931. Evolution in Mendellian populations. – Genetics
16: 97–159.
Wu, C.-I. and Davis, A. W. 1993. Evolution of postmating
reproductive isolation: the composite nature of Haldane’s
rule and its genetic bases. – Am. Nat. 142: 187–212.
Librado, P. and Rozas, J. 2009. DnaSP v5: a software for compre-
hensive analysis of DNA polymorphism data. – Bioinformatics
25: 1451–1452.
Mank, J. E., Vicoso, B., Berlin, S. and Charlesworth, B. 2010a.
Effective population size and the faster-x effect: empirical
results and their interpretation. – Evolution 64: 663–674.
Mank, J. E., Nam, K. and Ellegren, H. 2010b. Faster-Z evolution
is predominantly due to genetic drift. – Mol. Biol. Evol. 27:
Manthey, J. D., Klicka, J. and Spellman, G. M. 2011a.
Cryptic diversity in a widespread North American songbird:
phylogeography of the brown creeper (Certhia americana).
– Mol. Phylogenet. Evol. 58: 502–512.
Manthey, J. D., Klicka, J. and Spellman, G. M., 2011b. Isolation-
driven divergence: speciation in a widespread North American
songbird (Aves: Certhiidae). – Mol. Ecol. 20: 4371–4384.
Martin, D. and Rybicki, E. 2000. RDP: detection of recombination
amongst aligned sequences. – Bioinformatics 16: 562–563.
Martin, D. P., Posada, D., Crandall, K. A. and Williamson, C.
2005. A modified bootscan algorithm for automated identi-
fication of recombinant sequences and recombination
breakpoints. – AIDS Res. Hum. Retroviruses 21: 98–102.
Milne, I., Lindner, D., Bayer, M., Husmeier, D., McGuire, G.,
Marshall, D. F. and Wright, F. 2009. TOPALi v2: a rich graph-
ical interface for evolutionary analyses of multiple alignments
on HPC clusters and multi-core desktops. – Bioinformatics
25: 126–127.
Nei, M. 1987. Molecular evolutionary genetics. – Columbia Univ.
Padidam, M., Sawyer, S. and Fauquet, C. M. 1999. Possible
emergence of new geminiviruses by frequent recombination.
– Virology 265: 218–225.
Peach, W., duFeu, C. and McMeeking, J. 1995. Site tenacity
and survival rates of wrens Troglodytes troglodytes and
treecreepers Certhia familiaris in a Nottinghamshire wood.
– Ibis 137: 497–507.
Posada, D. and Crandall, K. A. 2001. Evaluation of methods
for detecting recombination from DNA sequences:
computer simulations. – Proc. Natl Acad. Sci. USA 98:
Sæther, S. A., Sætre, G. P., Borge, T., Wiley, C., Svedin, N.,
Andersson, G., Veen, T., Haavie, J., Servedio, M. R., Bures,
Supplementary material (Appendix JAV-00233 at www. ). Appendix 1.
... All sequences for the locus ALDO were identical and therefore p was zero (and thus removed from further analyses). Considering Le Conte's thrashers as a single unit, nucleotide diversity (p) was 0.0129 in mtDNA, Sex-linked markers could show reduced introgression and higher fixation levels relative to autosomal loci (Manthey andSpellman 2014, Oswald et al. 2016). Hence, we ran separate IMa2p analyses for Z-linked and autosomal loci using the same parameters and metrics as for combined analyses with the population migration rate (2Nm; Wright 1931). ...
... The Le Conte's thrasher represents such a species. In T. lecontei, divisions in mtDNA and nDNA distinguish T. l. arenicola, and T. l. lecontei plus T. l. macmillanorum documented in brown creepers Certhia americana (Manthey and Spellman 2014) and higher number of fixed Z-linked SNPs between Willet subspecies (Oswald et al. 2016). Fixed differences in most Z-linked loci is consistent with little to no gene flow in sex chromosomes. ...
... It is possible that because female birds are the heterogametic sex (ZW vs ZZ in males) Haldane's Rule may limit female driven gene flow (Haldane 1922), male sexual selection (Saether et al. 2007), and mutations on sex chromosomes having relatively large effects on hybrid fitness compared to those on autosomes in the 'large-X chromosome (in birds large-Z) effect' (Coyne and Orr 1989), thus accounting for an excess of differentiation and reduced gene flow in sex-linked loci. Although Le Conte's thrashers are assumed to be monogamous and remain paired with the same mate during their adult lifetime (Sheppard 1996), additional knowledge on breeding behavior, more comprehensive selection tests, and in particular more loci will aid in distinguishing between different evolutionary scenarios (Manthey andSpellman 2014, Oswald et al. 2016), and when (or if ) gene flow has occurred. ...
We evaluated geographic variation and subspecific taxonomy in the Le Conte's Thrasher (Toxostoma lecontei) by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140,000 years ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaino Thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention. This article is protected by copyright. All rights reserved.
... With new methods for obtaining reduced-representation libraries of the genome (for example, restriction digest-based methods, Miller et al., 2007 andultraconserved elements, Faircloth et al., 2012) for many individuals, phylogeographic studies may contain thousands of loci with dozens of individuals sampled. In songbirds, strong patterns of interchromosomal synteny (Kawakami et al., 2014), the published genome of the Zebra Finch (Taeniopygia guttata; Warren et al., 2010) and thousands of genetic markers across the genome allow the opportunity to investigate not only phylogeographic structure in a clade well known for its high levels of geographic differentiation (Manthey et al., 2011a), but also diversity and differentiation across chromosomes (Manthey and Spellman, 2014). ...
... There are two major lineages, split at 32°N latitude, within C. americana identified with both mitochondrial (mtDNA; Manthey et al., 2011a) and nuclear DNA (nDNA; Manthey et al., 2011b). Between the major lineages, there is also apparent quicker differentiation and reduced gene flow on the Z chromosome relative to autosomal loci (Manthey and Spellman, 2014). Finally, there is discordance between mtDNA and nDNA relationships between clades in the northern lineage (Manthey et al., 2011a, b); with thousands of loci across the genome, this discordance may be disentangled. ...
... In addition to broad chromosomal patterns, we also found that the level of differentiation between C. americana lineages on the Z chromosome was not an outlier when considered based on chromosome size (Figure 5a). This is in contrast to previous work in this species (Manthey and Spellman, 2014), as well as in contrast to other species (Carling andBrumfield, 2008, Ellegren et al., 2012), which generally show elevated differentiation in sex chromosomes compared with autosomes. Specifically, this was in stark contrast with up to 50-fold differences in levels of differentiation between the Z chromosome and autosomal background divergence levels between Ficedula species (Ellegren et al., 2012). ...
Full-text available
With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on ~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.Heredity advance online publication, 8 April 2015; doi:10.1038/hdy.2015.27.
... Examples of Z-linked loci being important in tracking and driving speciation and evolution in birds include European nightingales Luscinia spp. (Storchová et al. 2009) and Ficedula flycatchers (Ellegren et al. 2012), North American Anas ducks (Lavretsky et al. 2015), Passerina buntings Brumfield 2008, 2009), Certhia treecreepers (Manthey and Spellman 2014;, and in a comparative analysis of meliphagoid birds across hybrid zones in northeastern Australia (Peñalba et al. 2017) to name just a few. We should also consider physical rearrangements of entire blocks of chromosomes called chromosomal inversions. ...
The average person can name more bird species than they think, but do we really know what a bird “species” is? This open access book takes up several fascinating aspects of bird life to elucidate this basic concept in biology. From genetic and physiological basics to the phenomena of bird song and bird migration, it analyzes various interactions of birds – with their environment and other birds. Lastly, it shows imminent threats to birds in the Anthropocene, the era of global human impact. Although it seemed to be easy to define bird species, the advent of modern methods has challenged species definition and led to a multidisciplinary approach to classifying birds. One outstanding new toolbox comes with the more and more reasonably priced acquisition of whole-genome sequences that allow causative analyses of how bird species diversify. Speciation has reached a final stage when daughter species are reproductively isolated, but this stage is not easily detectable from the phenotype we observe. Culturally transmitted traits such as bird song seem to speed up speciation processes, while another behavioral trait, migration, helps birds to find food resources, and also coincides with higher chances of reaching new, inhabitable areas. In general, distribution is a major key to understanding speciation in birds. Examples of ecological speciation can be found in birds, and the constant interaction of birds with their biotic environment also contributes to evolutionary changes. In the Anthropocene, birds are confronted with rapid changes that are highly threatening for some species. Climate change forces birds to move their ranges, but may also disrupt well-established interactions between climate, vegetation, and food sources. This book brings together various disciplines involved in observing bird species come into existence, modify, and vanish. It is a rich resource for bird enthusiasts who want to understand various processes at the cutting edge of current research in more detail. At the same time it offers students the opportunity to see primarily unconnected, but booming big-data approaches such as genomics and biogeography meet in a topic of broad interest. Lastly, the book enables conservationists to better understand the uncertainties surrounding “species” as entities of protection.
... Third, numerous studies have shown that sex-linked (X or Z) loci introgress less readily than autosomal loci across hybrid zones (Hagen and Scribner 1989;Saetre et al 2003;Payseur et al. 2004;Storchová et al. 2010; see also Harrison and Larson 2014) and that X-linked introgressions have a proportionally higher effect on hybrid progeny compared to autosomal introgressions (Orr 1987;Coyne and Orr 1989). Lastly, evidence consistent with the dominance theory for HR comes from coalescent-based models showing that autosomes have historically been more permeable to gene flow than sex-linked loci in birds (Carling et al. 2010;Manthey and Spellman 2014), flies (Garrigan et al. 2012), mice (Geraldes et al. 2008), and even our own species' hybridization with Neanderthals (Sankararaman et al. 2014). Based on these results we agree with Payseur (2009), who noted "multilocus surveys of population differentiation have a bright future in speciation research." ...
Full-text available
There are few patterns in evolution that are as rigidly held as Haldane’s rule (HR), which states, “When in the first generation between hybrids between 2 species, 1 sex is absent, rare, or sterile, that sex is always the heterogametic sex.” Yet despite considerable attention for almost a century, questions persist as to how many independent examples exist and what is (are) the underlying genetic cause(s). Here, we review recent evidence extending HR to plants, where previously it has only been documented in animals. We also discuss recent comparative analyses that show much more variation in sex–chromosome composition than previously recognized, thus increasing the number of potential independent origins of HR dramatically. Finally, we review the standing of genetic theories proposed to explain HR in light of the new examples and new molecular understanding.
Full-text available
According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW-system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e. mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e. autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.
Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
Human beings have a strong, innate desire to classify and name things. We like things to be clear-cut. The way we approach classification of birds is as good an example as any of this. So it always comes as something of a surprise to non-ornithologists to learn that how we classify birds at the level of the species around us is still subject of so much at times fiery debate. Various chapters in this book approach this from different perspectives. In this chapter, the focus is on reminding us that evolution is an ongoing, dynamic process and that appreciating this evolution can help us make sense of why it is sometimes so complicated to pin names on birds and indeed many other organisms. This will take us into a few particular aspects of bird evolution. One will be the process of hybridization between populations that may or may not be of the same species or between species that may or may not be each other’s closest relatives. Another will concern the study of genetic diversity that exists within a species. In particular, we will examine what we have learned from the way that that diversity has come to be apportioned and distributed across the geographical range and landscapes inhabited by a species. These two areas have opened windows into the dynamics of evolution that give us new understanding of bird species. Genetic boundaries between species and subspecies are frequently very “leaky.” Only certain parts of the genome, the entire complement of genetic material in a species, may be contributing to the differences that we can see between bird species. If the chapter can convey to the reader that we must learn to think of birds as continually evolving evolutionary lineages, then it will have had some success.
Sky islands, or montane forest separated by different lowland habitats, are highly fragmented regions that potentially limit gene flow between isolated populations. In the sky islands of the Madrean Archipelago (Arizona, USA), various taxa display different phylogeographic patterns, from unrestricted gene flow among sky islands to complex patterns with multiple distinct lineages. Using genomic-level approaches allows the investigation of differential patterns of gene flow, selection, and genetic differentiation among chromosomes and specific genomic regions between sky island populations. Here, we used thousands of SNPs to investigate the putative contact zone of divergent Brown Creeper (Certhia americana) lineages in the Madrean Archipelago sky islands. We found the two lineages to be completely allopatric (during the breeding season) with a lack of hybridization and gene flow between lineages and no genetic structure among sky islands within lineages. Additionally, the two lineages inhabit different climatic and ecosystem conditions and have many local primary song dialects in the southern Arizona mountain ranges. We identified a positive relationship between genetic differentiation and chromosome size, but the sex chromosome (Z) was not found to be an outlier. Differential patterns of genetic differentiation per chromosome may be explained by genetic drift-possibly in conjunction with non-random mating and non-random gene flow-due to variance in recombination rates among chromosomes.
Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z-chromosome (females are heterogametic, ZW). We tested for elevated Z-differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal (Anas gracilis) and the dichromatic chestnut teal (A. castanea). Despite prominent morphological differences, these two species are genetically indistinguishable at both mitochondrial DNA (mean ΦST < 0.0001) and 17 autosomal loci (mean ΦST = 0.0056). However, we detected elevated Z-differentiation (mean ΦST = 0.271) and tentative evidence of an island of differentiation on the Z-chromosome. This elevated differentiation was explained by a high frequency of derived alleles in chestnut teal that were absent in grey teal, which parallels independent evidence for a gain in dichromatism from a monochromatic ancestor. Coalescent estimates of demographic history and simulations indicated that the elevated Z-differentiation was unlikely to be explained by neutral processes, but instead supported a role of divergent selection. We discuss evidence for models of speciation with gene flow versus adaptive divergence in the absence of gene flow and find that both hypotheses are plausible explanations of the data. Overall, these teal have the weakest background differentiation documented to date for a species showing a large Z-effect, and they are an excellent model species for studying speciation genomics and the evolution of sexual dichromatism.This article is protected by copyright. All rights reserved.
Relationships and species limits among the colourful Australian parrots known as rosellas (Platycercus) are contentious because of poorly understood patterns of parapatry, sympatry and hybridization as well as complex patterns of geographical replacement of phenotypic forms. Two subgenera are, however, conventionally recognized: Platycercus comprises the blue-cheeked crimson rosella complex (Crimson Rosella P. elegans and Green Rosella P. caledonicus), and Violania contains the remaining four currently recognized species (Pale-headed Rosella P. adscitus, Eastern Rosella P. eximius, Northern Rosella P. venustus, and Western Rosella P. icterotis). We used phylogenetic analysis of ten loci (one mitochondrial, eight autosomal and one Z-linked) and several individuals per nominal species primarily to examine relationships within the subgenera, especially the relationships and species limits within Violania. Of these, P. adscitus and P. eximius have long been considered sister species or conspecific due to a morphology-based hybrid zone and an early phylogenetic analysis of mitochondrial DNA restriction fragment length polymorphisms. The multilocus phylogenetic analysis presented here supports an alternative hypothesis aligning P. adscitus and P. venustus as sister species. Using divergence rates published in other avian studies, we estimated the divergence between P. venustus and P. adscitus at 0.0148 - 0.6124 MYA and that between the P. adscitus / P. venustus ancestor and P. eximius earlier at 0.1617 - 1.0816 MYA, both within the Pleistocene. Discordant topologies among gene and species trees are discussed and proposed to be the result of historical gene flow and/or incomplete lineage sorting (ILS). In particular, we suggest that discordance between mitochondrial and nuclear data may be the result of asymmetrical mitochondrial introgression from P. adscitus into P. eximius. The biogeographical implications of our findings are discussed relative to similarly distributed groups of birds. Copyright © 2015 Elsevier Inc. All rights reserved.
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F(ST) is frequently used as a summary of genetic differentiation among groups. It has been suggested that F(ST) depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of F(ST) on allele frequencies, however, has been elusive. Here, we examine the relationship between F(ST) and the frequency of the most frequent allele, demonstrating that the range of values that F(ST) can take is restricted considerably by the allele frequency distribution. For a two-population model, we derive strict bounds on F(ST) as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum F(ST) is ~0.3585. Further, F(ST) is restricted to values much less than 1 when M is low or high, and the contribution to the maximum F(ST) made by the most frequent allele is on average ~0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on F(ST) in terms of the homozygosity of the total population, finding that the mean maximum F(ST) given this homozygosity is 1 - ln 2≈0.3069. Our results provide a conceptual basis for understanding the dependence of F(ST) on allele frequencies and genetic diversity, and for interpreting the roles of these quantities in computations of F(ST) from population-genetic data. Further, our analysis suggests that many unusual observations of F(ST), including the relatively low F(ST) values in high-diversity human populations from Africa and the relatively low estimates of F(ST) for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of F(ST) on the properties of allele frequency distributions.
The neutral theory of molecular evolution predicts that regions of the genome that evolve at high rates, as revealed by interspecific DNA sequence comparisons, will also exhibit high levels of polymorphism within species. We present here a conservative statistical test of this prediction based on a constant-rate neutral model. The test requires data from an interspecific comparison of at least two regions of the genome and data on levels of intraspecific polymorphism in the same regions from at least one species. The model is rejected for data from the region encompassing the Adh locus and the 5′ flanking sequence of Drosophila melanogaster and Drosophila sechellia. The data depart from the model in a direction that is consistent with the presence of balanced polymorphism in the coding region.
In the famous last paragraph of On the Origin of Species, Darwin compared the “fixed law of gravity”, which causes the Earth to orbit the Sun, with the evolution of species by natural selection. This may be the first recorded case in biology of “physics envy”: the view that the proper task of the life sciences—in Darwin's case, evolutionary biology—is to emulate physics by establishing general laws and working out their consequences. Although we don't speak of “laws” in biology, we do have lawlike generalizations, including the near‐universality of the genetic code and the mechanism for translating DNA and RNA into proteins. This article is protected by copyright. All rights reserved.
Develops models of the rates of evolution at sex-linked and autosomal loci and of the rates of fixation of chromosomal rearrangements involving sex chromosomes and autosomes. Substitution of selectively favorable mutations often proceeds more rapidly for X- or Y-linked loci than for the autosomes, provided that mutations are recessive or partially recessive on average. -from Authors