Journal of Heredity Advance Access originally published online on July 14, 2006
Journal of Heredity 2006 97(4):389-402; doi:10.1093/jhered/esl011
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Different Post-Pleistocene Histories of Eurasian Parids
From the Bell Museum of Natural History, University of Minnesota, St Paul, MN 55108 (Pavlova and Zink); Burke Museum and Department of Zoology, University of Washington, Seattle, WA 98195-3010 (Rohwer); and Department of Biological Sciences, University of Alaska, Anchorage, AL 99508 (Drovetski). Alexandra Pavlova is now at the School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
Address correspondence to R. M. Zink, 100 Ecology Building, 1987 Upper Buford Circle, St Paul, MN 55108, or e-mail: zinkx003{at}umn.edu.
Previous phylogeographic studies of the great tit (Parus major) and the willow tit (Parus montanus) found a general absence of phylogeographic structure for both species and suggested that each species underwent range contraction during the last Ice Age and survived in relatively low numbers, P. major in southern Europe and P. montanus in southeastern Asia. However, prior studies did not sample the entire range of either species. We analyzed sequence data for the complete mitochondrial ND2 gene from 87 P. major and 139 P. montanus from 15 new Eurasian localities, both to test prior conclusions and to provide better coverage of each species' range. Our analyses confirmed the absence of phylogeographic structure in P. major and P. montanus and supported the prior refuge hypothesis for P. major. For P. montanus, we concluded that besides surviving the Ice Age in southeastern Asia, as previously hypothesized, it apparently sustained a relatively large population in northern Eurasian riverine thickets and then expanded eastward. Genetic diversity was low in P. major (
= 0.0012, h = 0.64) and moderate in P. montanus ( = 0.0021, h = 0.88), suggesting higher long-term effective population sizes and the older ages of populations in P. montanus. If molecular substitution rates are similar, P. montanus colonized its current Eurasian range earlier than P. major. Differences between prior studies and ours likely result from sampling gaps in earlier studies.
Phylogeographic studies have revealed that many North American and European species were strongly affected by Pleistocene glaciations (Hewitt 1996, 1999, 2004; Taberlet and others 1998). Relatively few studies, however, examine species with wide Eurasian distributions (Irwin and others 2001; Kvist and others 2001, 2003; Liebers and others 2001; Zink, Drovetski, and Rohwer 2002; Zink, Rohwer, and others 2002; Pavlova and others 2003; Zink and others 2003; Drovetski, Zink, Rohwer, and others 2004; Godoy and others 2004; Pavlova 2004; Pavlova, Zink, and Rohwer 2005; Pavlova, Zink, Rohwer, and others 2005) because of the difficulties in obtaining samples. As a result, many studies of Palearctic species sample the European part of the species' ranges but only include a few Asian samples. Such sampling gaps can affect the conclusions of phylogeographic studies (Zink and others 2003). In this paper, we analyze new and published mitochondrial DNA (mtDNA) sequences representing most of the range of 2 widespread Eurasian passerine birds, the great tit (Parus major) and the willow tit (Parus montanus). Our goals are to test prior conclusions about the recent histories of these species and their taxonomic status.
Parus major
In a review of morphological variation, Harrap and Quinn (1995) distinguished 3 major groups in the P. major species complex: major (yellow-bellied with green upperparts; 11 subspecies inhabiting Europe, northwest Africa, and northern Asia; Figure 1A), minor (whitish belly and green upperparts; 9 subspecies inhabiting southeast Russia, Japan, and northern Southeast Asia), and cinereus (whitish belly and blue-gray upperparts; 13 subspecies inhabiting northeast Iran, south Afghanistan, India, and Indonesia). A fourth group, the Turkestan tit (Parus bokharensis), is often included in the major group, but it is considered a species by Harrap and Quinn (1995). Parus bokharensis resembles cinereus but is slightly smaller and longer tailed and occurs in the lowlands of central Asia from Turkmenia to Mongolia (Cramp and Perrins 1993). Songs of the major group differ substantially from songs of the other groups (Ivankina and others 1997). Formozov and others (1993) suggested that major and bokharensis are the most distant from each other among the 4 groups based on morphological characters; however, their view was not supported by the mtDNA study of Kvist and others (2003), which found a clade consisting of 2 pairs of sister taxa, major and bokharensis and cinereus and minor. Thus, although some hybridization does occur where group ranges meet (Kerimov and Formozov 1986; Formozov and others 1993; Nazarenko and others 1999; Fedorov and others forthcoming), the 4 groups have had independent evolutionary histories and, therefore, should be considered phylogenetic species (Kvist and others 2003). In this paper, we consider the great tit (P. major), the Turkestan tit (P. bokharensis), and the Japanese tit (Parus minor) separate species (we lack Parus cinereus), as do some other authors (Stepanyan 2003).
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Kvist and others (1999) studied genetic variation in 6 European populations of P. major using sequence data from the complete mitochondrial (mtDNA) control region (CR) for 68 birds (Figure 1A, Table 1). They found an absence of phylogeographic structure and extensive gene flow among populations, for which they inferred recent demographic expansions. Kvist and others (1999) hypothesized that the Balkans was a refugium during the last glacial maximum (20 000 years ago) and that P. major subsequently expanded rapidly to northern Europe. More recently, Kvist and others (2003) examined partial CR sequences of 125 P. major expanding the initial sampling to Portugal and the United Kingdom in Europe and to 3 Asian and 1 African localities (open circles in Figure 1A, Table 1); they also included sequences of 3 individuals of P. bokharensis from Kirghizia and 44 individuals of P. minor from 4 southeastern Asian populations (Figure 1A, Table 1). Kvist and others (2003) found low genetic diversity within P. major and concluded that the genetic variation within populations of P. major was reduced drastically because of population bottlenecks during Ice Age range contractions. Although the starlike haplotype network of Kvist and others (2003; their Figure 2) suggested no overall phylogeographic structure, their analysis of molecular variance (AMOVA) showed some overall population structure (
ST = 0.12) and pairwise population ST values for the geographically isolated populations from Kirghizia and the United Kingdom were large and significant. Based on higher genetic diversity in the 3 individuals of P. bokharensis, it was concluded that P. bokharensis was historically stable, whereas both P. major and P. minor experienced Late Pleistocene or Holocene population reductions and subsequent expansions. Kvist and others (2003) also suggested that P. major had a larger and more recent population expansion than P. minor.
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Parus montanus
This species ranges from northeastern France through central and northern Europe and Russia to the Pacific coast (Cramp and Perrins 1993, Figure 1B). Geographic variation in morphology is clinal and connects most of the continental subspecies, which also differ in song types and coloration (Harrap and Quinn 1995). Harrap and Quinn (1995) divided P. montanus into 3 subspecies groups: salicarius (northern Eurasia, 6 subspecies), kamtschatkensis (Pacific rim in eastern Asia, 4 subspecies), and montanus (mountains of central Europe, 1 subspecies); they considered the songar tit (Parus songarus) of central Asia a separate species, as we do in this paper.
Kvist and others (2001) and Salzburger and others (2002), using sequences of the mitochondrial CR and cytochrome b, respectively, found no mtDNA structuring associated with subspecies groups within P. montanus, whereas the songar tit, considered by them as subspecies of P. montanus, was found to be polyphyletic and consisting of 3 distinct lineages: weigoldicus, affinis, and songarus. On the basis of close relationships among 6 Eurasian subspecies of P. montanus, Salzburger and others (2002) suggested that this species spread over major parts of Eurasia during the Pleistocene and underwent rapid morphological and vocal divergence. Kvist and others (1998) compared complete mitochondrial CR sequences from Finland and Swedish populations and concluded that individuals from both localities belong to one panmictic population with high long-term effective population size. Later, Kvist and others (2001) studied partial CR sequences of birds from 6 western European localities, 6 samples from eastern Asia, and 1 sample from the Urals (open circles in Figure 1B, Table 2) and found no phylogeographic structure; however, their AMOVA showed that populations were subdivided overall (ST = 0.15), and all pairwise population ST values for Japan and most ST values for Latvia were large and significant. Kvist and others (2001) attributed the general lack of phylogeographic structure to homogeneous habitat throughout the distribution, absence of geographic barriers, high gene flow, and a high long-term effective population size and, based on trend of westward decrease in genetic diversity, suggested that P. montanus expanded through the Palearctic from southeastern Asia after the last Ice Ages.
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Summary of Previous Work on Parid Phylogeography
Several studies have shown a general lack of phylogeographic structure and evidence of overall population subdivision in P. major and P. montanus (sensu strictu). However, except for the Urals, samples from eastern Europe and western Asia were lacking (open circles in Figure 1 indicate prior samples). Species-level evolutionary conclusions should not be made with confidence until the complete geographic range is sampled. This concern motivated us to add new localities (black circles in Figure 1) from previously unstudied areas. If the conclusions of Kvist and others (2001, 2003) are correct, then our expanded analyses should reveal 1) a general absence of geographic structure on the haplotypes trees of both species, 2) a decrease in genetic diversity consistent with the direction of expansion: eastward and northward in P. major and westward and northward in P. montanus, 3) signatures of expansion for populations of both species, and 4) earlier expansions in southeastern populations of P. montanus relative to the northern and western populations. Because our new samples overlap to some degree with those used in the studies reviewed above, we chose to sequence the mitochondrial coding gene ND2. Thus, in addition to testing prior phylogeographic conclusions, we were able to compare genetic estimates derived from the noncoding CR with those from ND2.
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Materials and Methods |
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 Top Materials and Methods Results and DiscussionReferences |
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New Sampling
We analyzed 87 individuals of P. major from 15 Eurasian localities, 4 individuals of P. bokharensis from Almaty, and 29 individuals of P. minor from Primor'e (black circles in Figure 1A, Table 1). For P. montanus, we analyzed 139 individuals from 17 localities (Figure 1B, Table 2). We used the marsh tit Parus palustris (GenBank number AY734248) as an out-group for the haplotype tree of P. montanus and P. minor for P. major. All birds were collected during the breeding season. From nearly all specimens, a study skin and spread wing were preserved and deposited at the Burke Museum, University of Washington, Seattle; the Moscow State University Zoological Museum, Moscow, Russia; the Bell Museum, University of Minnesota, St Paul; or the State Darwin Museum, Moscow, Russia. Tissue samples were preserved in the field either in 96% ethanol or in lysis buffer (Longmire and others 1997) or frozen in liquid nitrogen.
Molecular Laboratory Methods
Isolation and purification of DNA was performed using QIAamp Tissue Kit (Qiagen, Valencia, CA). Polymerase chain reaction (PCR) (Saiki and others 1988) with Perkin-Elmer PCR reagents and primers L5215 (Hackett 1996) and H1064 (Drovetski, Zink, Fadeev, and others 2004) was used to amplify the complete ND2 gene; PCR conditions are explained in Drovetski, Zink, Fadeev, and others (2004). PCR products were cleaned with Qiaquick PCR Purification Kit (Qiagen) and directly sequenced on ABI 3700 automated sequencer using BIGDYE versions 3.0 and 3.1 chemistry (Applied Biosystems, Foster City, CA) and primers L5215, H1064, L347 (Drovetski, Zink, Fadeev, and others 2004), and H5578 (Hackett 1996).
Data Analysis
Sequences were aligned and edited in SEQUENCHER 3.1.1 (Gene Codes Corporation, Ann Arbor, MI). Sequence data have been deposited in GenBank (Accession numbers AY732613–AY732729, AY734249–AY734251, and AY732869–AY733007). Mitochondrial origin of sequenced DNA fragments was supported by the absence of stop codons and the existence of a large number of haplotypes, which are inconsistent with nuclear copies (Zhang and Hewitt 1996). A matrix of variable sites was used as input for constructing a median-joining network (Bandelt and others 1999) using software NETWORK version 4.110 (http://www.fluxus-engineering.com) assigning equal weights to all sites and with default value of epsilon = 0.
Maximum likelihood (ML) model and parameters were determined by the hierarchical likelihood ratio test in MODELTEST 3.06 (Posada and Crandall 1998). PAUP* (Swofford 2000) and PHYML (Guindon and Gascuel 2003) were used to perform ML tree searches. SEQBOOT and CONSENSE were used from the PHYLIP program package (Felsenstein 1993). SEQBOOT version 3.5c was used to generate 100 bootstrapped sets of data from which ML trees were constructed in PHYML. Then, CONSENSE version 3.5c was used to compute a majority rule consensus tree.
DNASP version 4.00 (Rozas and others 2003) was used to calculate the number of haplotypes in populations, nucleotide diversity (, Nei 1987; Equation 10.5), haplotype diversity (h; Nei 1987; Equation 8.4), and theta (
= 2Neµ, where Ne is the effective population size and µ is the mutation rate) from the number of polymorphic sites per nucleotide (Tajima 1996) and to perform the R2 test for detecting population growth (Ramos-Onsins and Rozas 2002). We used ARLEQUIN version 2.000 (Schneider and others 2000) to perform an AMOVA (Excoffier and others 1992) taking into account haplotype frequencies and the distances between haplotypes, to compute pairwise population ST, mismatch distributions, time since population expansion (
), effective population sizes before (0) and after (1) expansion, and Tajima's D (Tajima 1996) and Fu's Fs (Fu 1997) tests of selective neutrality for localities with sample sizes greater than 10 individuals (in some cases, samples were pooled if they were not significantly differentiated). The latter 2 tests were used as indicators of population expansion. Sites with ambiguous characters were removed. To test the empirical mismatch distribution against a model of sudden expansion, we used the generalized nonlinear least squares approach (Schneider and Excoffier 1999) implemented in ARLEQUIN. We compared our estimates of with those of Kvist and others (2001, 2003) and regressed values of against latitude and longitude for samples of 3 or more individuals expecting smaller values to be observed on the leading edge of population expansion (Hewitt 1999, 2000).
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Results and Discussion |
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TopMaterials and MethodsResults and DiscussionReferences |
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The Great Tit P. major
Genetic Variability and Gene Flow
We analyzed 1039 aligned nucleotides of ND2 after removing sites with missing characters. The 34 polymorphic sites (9 of them parsimony informative) resolved 24 haplotypes among the 87 individuals (Table 1). The most common haplotype (haplotype A in Figure 2) was shared by 52 individuals (60% of all sampled individuals) from 13 populations: Norway (1 individual), Kursk (2), Smolensk (2), Crimea (1), Krasnodar (4), Moscow (16), Medvedevo (2), Astrakhan' (4), Krasnoyarsk (1), Irkutsk (5), Buryatiya (4), Mongolia (3), and Magadan (7). Three more haplotypes were shared among localities (Figure 2). Overall haplotype diversity was 0.638 and ranged from 0 in Buryatiya, Mongolia, and Magadan, where all individuals shared the most common haplotype, to 1 in Norway and Crimea (Table 1). Overall nucleotide diversity (
) averaged 0.0012 and ranged from 0.0 in Buryatiya, Mongolia, and Magadan to 0.0026 in Crimea (Table 1). Northern populations had lower , both for our data and for those of Kvist and others (2003) (Figure 3A), but this trend was not significant (P > 0.05). Our data, but not those of Kvist and others (2003), showed a significant trend toward eastern birds having lower (R2 = 0.43, P = 0.03) (Figure 3B), suggesting eastward dispersal. A general lack of population subdivision was suggested by the overall nonsignificant ST value (P > 0.05, Table 1). However, several pairwise population comparisons yielded significant (P < 0.05) ST values: Krasnodar–Magadan (ST = 0.07), Crimea–Buryatiya (0.11), and Astrakhan'–Irkutsk (0.05), indicating that gene flow between eastern and western populations might be restricted.
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Molecular Phylogenetic Analysis and Phylogeography
MODELTEST 3.06 indicated TrN + G (Tamura and Nei 1993) with alpha = 0.0069 as the best-fit model of sequence evolution. On the ML tree found by PHYML (not shown), all 24 haplotypes of P. minor clustered together (this clade was recovered by 100% of 100 ML bootstrapped trees), as well as the 2 haplotypes of P. bokharensis from Almaty (99% bootstrap support). However, the P. major clade received only 69% bootstrap support and was not recovered by the ML tree found by PAUP* because the P. bokharensis clade was embedded in it, making P. major paraphyletic. On the haplotype network (Figure 2), P. bokharensis was separated from P. major by 10 mutational steps. Intraspecific genealogies can be multifurcating due to ancestral and descendant haplotypes coexisting in populations, which violates the assumption of bifurcating trees employed in ML algorithm (Posada and Crandall 2001). Thus, the network likely provides a better estimate of among-haplotype relationships, and we conclude that both P. major and P. bokharensis are evolutionarily independent lineages.
In general, our results (Figure 2) confirm and extend those of Kvist and others (1999, 2003) that P. major is not structured geographically. This inference is strengthened by the observation that the most common haplotype was shared by more than a third of the individuals and distributed throughout Eurasia (Table 1), including our new sites. For example, most (20 of 24) individuals from our Asian localities (Yekaterinburg, Krasnoyarsk, Irkutsk, Buryatiya, Mongolia, and Magadan) shared the most common haplotype. The widespread occurrence of common haplotypes is explicable given known patterns of dispersal. Although young P. major normally disperse less than 10 km on average from their natal grounds, "northern and eastern populations are eruptive migrants, moving in highly variable numbers depending on the food supply ..." (Harrap and Quinn 1995, p. 356), and some invading birds remain to breed in the wintering areas. This dispersal pattern can explain the general absence of differentiation in continental tits.
The insignificant overall ST for our data also suggests that P. major is not geographically subdivided, although several significant pairwise values suggested restricted gene flow between some eastern and western populations. Kvist and others (2003) also found evidence of differentiation for 2 geographically isolated populations, United Kingdom and Kirghizia, for which significant pairwise ST values were found. This local differentiation is apparently attributable to relatively low natal dispersal distances (Verhulst and others 1997). In addition, 19 of 20 unique haplotypes were sampled from European populations (Figure 2). These results support the hypothesis of recent colonization of eastern Eurasia and can account for some of the east–west population differences.
Therefore, although earlier studies were limited in their sampling of the range, the expanded analysis presented here corroborates the hypothesis that there is little geographic structure across the huge Palearctic range of P. major. The general absence of phylogeographic structure as the result of postglacial range expansion and low genetic diversity was reported for 2 northern species of North American chickadees, Poecile atricapillus and Poecile hudsonicus (Gill and others 1993). Other forest-dwelling birds also appear to lack phylogeographic structure across much of northern Eurasia (e.g., Zink, Drovetski, and Rohwer 2002; Zink, Rohwer, and others 2002).
The mtDNA data appear to conflict with 2 recent studies from the United Kingdom that revealed the existence of natural selection acting on local differences in life-history traits. Postma and van Noordwijk (2005) discovered differences in clutch size between subpopulations separated by only a few kilometers. Garant and others (2005) discovered that the mean mass of P. major decreased in one part of Wytham woods, whereas clutch size remained constant to the north. A significant genetic component to variation in these fitness or fitness-linked traits was documented in both studies. If these represented genome-wide patterns of differentiation, the mtDNA tree should have revealed more structure. Thus, the mtDNA data suggest that these local adaptations are very recently evolved.
Population Expansion
Kvist and others (2003) suggested that P. major populations underwent a drastic reduction in size as a result of range contraction during the last glacial maximum. Survival in low numbers in a small southwestern refugium (possibly Balkans, Kvist and others 1999) was thought to have been followed by northeastward range expansion and subsequent demographic expansion. Although many of our individual samples are small, our mismatch distributions and values of Tajima's D, Fu's Fs, and R2 are consistent with these hypotheses of population and range expansion (Table 3, Figure 4), as expected for north temperate populations (Hewitt 2004).
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To test for the effects of natural selection, Zink (2005) analyzed our data set using 2 partitions of the ND2 gene (surface and transmembrane portions and synonymous–nonsynonymous sites). Both partitions yielded similar estimates of
ST, which suggested demographic expansion as the cause of the shallow tree for P. major and not directional or stabilizing natural selection (Zink 2005).
Notes on Evolutionary History of P. bokharensis
Kvist and others (2003) suggested that there was less or no historic habitat reduction for P. bokharensis because it prefers deserts and semideserts, which is "the same kind of environment that existed during the Ice Ages within its present range" based on the reconstruction by Adams (1997). The estimate of Kvist and others (2003) of (from 3 individuals) for P. bokharensis led them to conclude that "populations have been stable for a long time because ... [they] ... possess more diversity than the minor and major groups." We did not find a higher in P. bokharensis with our sample of 4 birds. We suggest more samples are needed to clarify the history of P. bokharensis.
The Willow Tit P. montanus
Genetic Variability and Gene Flow
We analyzed 1039 aligned bp of ND2 after removing sites with ambiguous characters. The 63 polymorphic sites (26 parsimony informative) resolved 58 haplotypes among the 139 individuals (Table 2). The most common haplotype (haplotype A in Figure 5) was shared by 44 individuals (32% of all individuals) from 12 populations: Moscow (N = 2), Medvedevo (1), Mezen' (2), Noyabr'sk (1), Gorno-Altay (2), Tyva (1), Irkutsk (11), Buryatiya (8), Mongolia (3), Primor'e (5), Khabarovsk (2), and Magadan (6) (Figure 5). Two other common haplotypes were found: haplotype B (Figure 5) had a restricted Far Eastern distribution and occurred in 13 individuals from Kamchatka, Magadan, and Anadyr' and haplotype C was shared by 12 individuals from Mezen', Noyabr'sk, Irkutsk, Buryatiya, Mongolia, Primor'e, and Khabarovsk. Several more haplotypes were shared among populations (Figure 5). The occurrence of widespread haplotypes indicates considerable recent gene flow.
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Overall haplotype diversity (0.88) was moderate and ranged from 0.38 in Kamchatka to 1 in Medvedevo (Table 2). Overall nucleotide diversity was 0.0021 and ranged from 0.0004 in Anadyr' to 0.0032 in Mezen' (Table 2). Relatively high genetic diversity within P. montanus and the relatively large number of haplotypes found in our data and those of Kvist and others (2001) (Table 2) suggest a high long-term effective population size and an absence of recent bottlenecks.
Regressions of on latitude were not significant (P > 0.05) for our data or for those of Kvist and others (2001) (Figure 3C). Longitude explained 60% of the variance of in our data with eastern birds having lower (R2 = 0.6, P < 0.05), but no such trend was found for the data of Kvist and others (2001) (Figure 3D). Kvist and others (2001) reported a westward decrease in nucleotide diversity for salicarius group (which includes most of the species' distribution excluding Kamchatka, Sakhalin, and Japan), from which they concluded that during the last Ice Ages P. montanus occupied large regions of the southeastern Palearctic and colonized the European (western) part of the range from the east. However, our regression analysis of their nucleotide diversity data did not find this trend to be a statistically significant (with or without Kamchatka, Sakhalin, and Japan). Furthermore, our data show a significant trend in which the eastern birds have lower nucleotide diversity (Figure 3D), which might be a trace of past eastward range expansion. This does not mean, however, that our results contradict those of Kvist and others (2001). Low genetic diversity in European samples is expected because during last glacial maximum a large part of western Europe was under glacial ice and was recolonized recently. As Figure 1 demonstrates, the western samples of P. montanus of Kvist and others (2001) are from western Europe, and the eastward increase of nucleotide diversity might have resulted from their sampling design. The discrepancy in interpretation reinforces the need to have adequate geographic coverage.
Molecular Phylogenetic Analysis and Phylogeography
MODELTEST 3.06 suggested TrN + G (Tamura and Nei 1993) with alpha = 0.0153 as a most probable model of sequence evolution. This was the same model selected for the P. major group, suggesting similar sequence evolution of ND2 gene in different parids. The monophyly of P. montanus was supported by 100% of 100 ML bootstrap support replicates. The ML haplotype tree (not shown) was geographically unstructured, which can be seen in the network (Figure 5). Kvist and others (2001) also found a geographically unstructured haplotype network and attributed it to high gene flow. However, they also suggested that gene flow might not be currently high because of geographic differences in morphology and voice. Our haplotype network (Figure 5) shows that some haplotypes are restricted to Asia, suggesting limited gene exchange for some eastern localities. Furthermore, our AMOVA showed that geographic localities explain 10.8% of the total variation (P < 0.05). Most pairwise ST values involving Anadyr' (range 0–0.62) and Kamchatka (range 0–0.37) were large and significant (Table 4), indicating restricted or no gene flow between these and more western populations. Zink (2005) explored the nature of high ST values for these populations and found that they occurred because of a replacement substitution at base position 452 that was shared by all Anadyr' individuals and 4 of 5 birds from Kamchatka (haplotype B and 2 adjacent haplotypes from Anadyr' in Figure 5). Zink (2005) pointed out that although significant ST values might be a signature of incipient divergence caused by geographic isolation, they also might indicate a selection for a new favorable haplotype. Because only a single substitution is involved, a definitive conclusion is unwarranted. Several pairwise ST values involving Medvedevo (range 0–0.18) were also significant (Table 4), further supporting restricted gene flow between western and eastern populations. Significant pairwise ST values that are found for 2 northeastern populations (Anadyr' and Kamchatka, subspecies anadyrensis and kamtchatkensis) and the population from Japan (subspecies restrictus), Medvedevo, and Latvia (both belong to subspecies borealis), suggest that some populations of P. montanus are differentiated.
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Populations diverging from a common ancestor go through a series of stages represented by gene trees that are polyphyletic, then paraphyletic, and finally reciprocally monophyletic with respect to geography (Avise 2000). The existence of significant
ST values and a haplotype tree that is not reciprocally monophyletic, but has some limited differentiation, suggests that P. montanus is at an intermediate stage of differentiation. The pattern of incomplete genetic differentiation coincides in part with phenotypic (subspecific) divergence.
Population and Range Expansion
Kvist and others (2001) suggested that during Pleistocene cooling P. montanus was restricted to southeastern Asia and colonized Eurasia (westward) when the climate warmed. However, if P. montanus's range expanded from a refugium, then a large number of haplotypes from the refugial population is expected to be unique and most haplotypes from recently colonized areas are expected to be closely related to the common haplotype. Such a pattern was observed for P. major (Figure 2), consistent with the findings of Kvist and others (2003). However, on haplotype networks for P. montanus (Figure 5 in this paper and Figure 2 in Kvist and others [2001]), haplotypes from the western and most eastern, potentially refugial, populations were randomly distributed (although in Kvist and others 2001 no eastern individuals shared the most common haplotype). Reconstructions of biomes during the last glacial maximum based on pollen and plant macrofossils (Tarasov and others 1999) suggest that much of northeastern Europe and northwestern Asia were covered by tundra. Although P. montanus typically breeds in coniferous and mixed forests, it also inhabits woody shrubs and riverine thickets extending to the tree line in northern Eurasia and in mountainous regions (Harrap and Quinn 1995). Thus, Pleistocene tundra in northern Eurasia could have provided suitable habitats for P. montanus. The existence of substantial genetic diversity in western populations (see Figure 4 for comparison with P. major) suggests that P. montanus, unlike P. major, was not subjected to drastic range contractions and during climate warming could have expanded eastward, as suggested by our data, as well as westward to Europe, as Kvist and others (2001) suggested. It is also possible that historic range of P. montanus was split during the last Pleistocene cooling and some birds survived in refugial forests of eastern Asia.
The mtDNA data are consistent with the hypothesis of range and population expansion. Mismatch distributions (Figure 4) for P. montanus populations did not differ from the model of sudden population expansion and were unimodal for all localities except Irkutsk. Population growth was also suggested by most values of Tajima's D, Fu's Fs, and R2 for all populations except Buryatiya. Thus, both P. major and P. montanus appear to have responded to post–Ice Age habitat amelioration by range and population expansion, although as discussed below, the details differ.
Different Evolutionary Histories of P. major, P. minor, and P. montanus
During the last glacial maximum, some broadleaved forests of southeastern Asia were replaced by grassland vegetation. However, this part of the continent also contained several large refugial forests (Adams 1997) and, therefore, was a potential refuge for forest-dwelling birds. Although P. montanus, like P. major and P. minor, is a cavity nester and its range largely overlaps with that of P. major, the evolutionary history of P. montanus likely differed from that of its congeners, as evidenced by higher values of , , and h and the low percentage of individuals sharing a common haplotype (Table 5). A significant range restriction associated with Pleistocene cooling would be expected for P. major because they require forested habitats and do not live in the brushy habitats of land underlain with permafrost. Eastward decrease of genetic diversity (Figure 3B) and low genetic diversity suggest that P. major might have survived Pleistocene glaciations in small numbers in refugial forests of southern Europe and subsequently expanded into eastern Eurasia. In contrast to P. major, P. montanus, whose range extends farther north, did not undergo as severe a population bottleneck but instead survived in relatively large numbers in narrow riparian thickets in the widespread north Eurasian ice-free areas where large river valleys were free of permafrost, as well as in refugial forests of southeastern Asia.
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The present range of P. minor is restricted to southeastern Asia, and it is thought that the species only recently has been expanding northward (Smirenskiy 1986; Harrap and Quinn 1995). In fact, all but 5 haplotypes of P. minor in Kvist and others (2003) were unique and clustered according to their geographic localities on the haplotype network (their Figure 1), whereas only 2 of the 5 common haplotypes were shared between populations. A nonrandom distribution of haplotypes and the large significant overall
ST for P. minor (0.28, Table 5) indicate significant population subdivision, inconsistent with high gene flow expected from range expansion. For our only sample of P. minor (from Primor'e), significantly negative Tajima's D and Fu's Fs, significant R2 value (Table 3), and a starlike network where 46% individuals shared the most common haplotype (Figure 2) indicated population growth, consistent with recent colonization of Primor'e.
On the basis of similar nucleotide diversity for P. major and P. minor, but higher theta within P. major (the results consistent with our findings, Table 5), Kvist and others (2003) suggested a greater degree of population expansion in P. major than in P. minor because theta is more influenced by current population size, whereas reflects the historic size (Tajima 1989). Given that the range of P. major is roughly 4 times greater than that of P. minor, this conclusion is not surprising. Time since expansion (, Table 5) was small in P. major, intermediate in P. minor, and large in P. montanus for all data sets, indicating that expansion in P. major was relatively recent. In fact, range expansion of P. major is known to have mirrored the expansion of human settlements (Harrap and Quinn 1995), and in some regions of the Russian Far East, the species' presence is restricted to human habitations. In addition, introgression of major haplotypes into minor populations in the Amur region hybrid zone and absence of foreign haplotypes in allopatric P. minor populations provide indirect evidence toward high philopatry in P. minor (Fedorov and others forthcoming).
Thus, the genetic analyses of 3 codistributed sedentary parids suggest that each species responded differently to the environmental changes of the Ice Ages. These different genetic signatures are likely a result of differences in habitat use and dispersal abilities.
Comparison of Genetic Parameters Derived from CR and ND2
Regions of the mtDNA genome are known to evolve at different rates, owing in part to selective constraints. The CR is often considered the most variable, although this is not always the case (Ruokonen and Kvist 2002). Despite the potential for different regions of mtDNA to evolve at different rates, the entire gene has a single history owing to linkage. Nonetheless, it is of interest to make direct comparisons of different gene regions as studies often compare levels of variability across gene regions (Ruokonen and Kvist 2002). For the 5 European populations of P. major, estimates of nucleotide diversity were on average 1.64 times higher when computed from the partial 5'-end of the CR (Kvist and others 2003) than those calculated from the complete CR sequences (Kvist and others 1999) (Table 1), indicating that within species the 5'-end of the mitochondrial CR is more variable than the 3'-end. This result was reported earlier for intraspecific comparisons in P. major, Parus caeruleus, and P. montanus (Ruokonen and Kvist 2002). However, for the 2 Scandinavian populations of P. montanus studied by Kvist and others (1998, 2001), the results were not consistent: Finland was higher when estimated from partial (5'-end) CR, whereas Sweden was higher when estimated from complete CR sequences. Such inconsistency in the relative distribution of variation in CR sequences makes it hard to compare estimates of obtained from different mitochondrial gene regions. Although Ruokonen and Kvist (2002) suggested that the distribution of variation in CR is similar within genera, nucleotide diversity estimated from the 3'-end of the CR sequences for P. major, P. minor, and P. montanus (A Pavlova, RM Zink, S Rohwer, and S Drovetski, unpublished data; GenBank sequence numbers AY732496–AY732612 and AY732730–732868) yielded comparative results very different than those obtained from ND2 for the same sets of individuals. For example, from the 3'-end of CR was 0.0007, 0.0034, and 0.0026 and was 0.0046, 0.0114, and 0.0125 for P. major, P. minor, and P. montanus, respectively, whereas estimates of from ND2 or 5'-end of CR were similarly low for P. major and P. minor and was smallest in P. minor (Table 5). This example demonstrates that different parts of mitochondrial genome, and even parts of the same gene region, evolve with different rates in different taxa (even within genera), and care must be used when interpreting results. Thus, molecular clock rates calibrated for coding genes should not be applied for CR data to avoid substantial overestimation of the ages of population/species splits. Furthermore, calibrations for different parts of the CR are not general.
Values of nucleotide diversity estimated from our ND2 data were consistently lower than those calculated from the partial CR data of Kvist and others (2001, 2003). For the 4 eastern populations of P. montanus (Magadan, Kamchatka, Khabarovsk [Amur], and Primor'e [Ussuri]), our samples and those of Kvist and others (2001) overlapped (Figure 1B, Table 2). Comparisons of estimates of genetic diversity calculated from ND2 and partial CR for these populations showed that estimates of from partial CR are on average 2.9 times higher than from ND2 and estimates of h are 1.4 times higher from partial CR than from ND2 (Table 5). Therefore, for Parus species, the 5'-end of CR yields more intraspecific variation than either complete CR or ND2, and estimates of genetic diversity obtained from different genes cannot be compared directly.
Because it is always possible that CR sequences are nuclear in origin, it is important to confirm general findings with a coding gene such as ND2, which can be more easily checked for mitochondrial authenticity. Genetic parameters estimated from ND2 showed a pattern similar to the one from partial CR studies of Kvist and colleagues (Table 5). In all studies, haplotype diversity was low in P. major and higher in P. minor and P. montanus, whereas nucleotide diversity was similar in P. major and P. minor and higher in P. montanus (Table 5). For P. montanus, we also computed genetic parameters for our ND2 data removing 3 sites (Anadyr', Kamchatka, and Medvedevo) that had the majority of significant pairwise ST values (Table 5) because population substructure, found both in Kvist and others (2003) and in our study (Table 4), could confound the estimation of these parameters. The relative values of the genetic parameters did not change. Thus, although absolute values for parameters cannot be directly compared across gene regions, the overall phylogeographic pattern is consistent.
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Acknowledgments |
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We are grateful to B. Eddy, H. Furguson, and to the late G. Eddy for funding fieldwork. Additional support came from the National Science Foundation (DEB 9707496 and DEB 0212832) and the Dayton-Wilkie Natural History fund. Tissue samples were provided by Burke Museum of Natural History and Culture, University of Washington; Moscow State University Zoological Museum, Moscow, Russia; and the Bell Museum of Natural History, University of Minnesota. We thank the Burke Museum for curatorial assistance and M. Westberg for laboratory assistance. We also thank A. Andreev, V. Andreev, Yu. Lohman, D. Banin, I. Karagodin, Ya. Red'kin, B. Schmidt, V. Rohwer, C. S. Wood, X. Pu, V. Masterov, R. Faucett, G. Voelker, V. Sotnikov, S. Birks, B. Barber, I. Fadeev, E. Nesterov, E. Koblik, and A. Jones for logistical help with expeditions and collecting.
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Footnotes |
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Corresponding Editor: Rob Fleischer
Received March 9, 2005
Accepted May 21, 2006
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References |
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Adams JM. (1997) Global land environments since the last interglacial (Oak Ridge National Laboratory, Oak Ridge, TN) Available from: http://www.esd.ornl.gov/projects/qen/nerc.html.
Avise JC. (2000) Phylogeography: The history and formation of species (Harvard University Press, Cambridge, MA).
Bandelt H-J, Forster P, Röhl A. (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48.[Abstract]
Cramp S and Perrins CM. (1993) Handbook of the birds of Europe, the Middle East and North Africa (Oxford University Press, Oxford) Volume 7:.
Drovetski SV, Zink RM, Fadeev IV, Nesterov YV, Koblik YA, Red'kin YA, Rohwer S. (2004) Mitochondrial phylogeny of Locustella and related genera. J Avian Biol 35:105–10.[CrossRef]
Drovetski SV, Zink RM, Rohwer S, Fadeev IV, Nesterov YV, Karagodin I, Red'kin YA. (2004) Complex biogeographic history of a holarctic passerine. Proc R Soc Lond B Biol Sci 271:545–51.[CrossRef][Medline]
Excoffier L, Smouse PE, Quattro JM. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–91.[Abstract]
Fedorov VV, Formozov NA, Surin VL, Valchuk OP, Kerimov AB. Genetic consequences of hybridization between Parus major and P. minor in the Middle Amurland. Zool Zhurnal [in Russian]. Forthcoming.
Felsenstein J. (1993) PHYLIP. Version 3.5. Available from: http://evolution.genetics.washington.edu/phylip.html. Accessed 2005 Feb 24.
Formozov NA, Kerimov AB, Lopatin VV. (1993) New hybridization zone of the great titmouse and Parus bokharensis in Kazakhstan and relationships in forms of Parus major superspecies. In Rossomolino OL (Ed.). Hybridization and the problem of species in vertebrates (Archives of the Zoological Museum Moscow State University, Moscow, Russia) pp. 118–46 [in Russian].
Fu Y-X. (1997) Statistical tests of neutrality against population growth, hitchhiking and background selection. Genetics 147:915–25.[Abstract]
Garant D, Kruuk LEB, Wilkin TA, McCleery RH, Sheldon BC. (2005) Evolution driven by differential dispersal within a wild bird population. Nature 433:60–5.[CrossRef][Medline]
Gill FB, Mostrom AM, Mack AL. (1993) Speciation in North American chickadees: I. Patterns of mtDNA genetic divergence. Evolution 47:195–212.[CrossRef][Web of Science]
Godoy JA, Negro JJ, Hiraldo F, Donáza JA. (2004) Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L.) as revealed by mitochondrial DNA. Mol Ecol 13:371–90.[CrossRef][Medline]
Guindon S and Gascuel O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704.
Hackett SJ. (1996) Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol Phylogenet Evol 5:368–82.[CrossRef][Web of Science][Medline]
Harrap S and Quinn D. (1995) Chickadees, tits, nuthatches, and treecreepers (Princeton University Press, Princeton, NJ).
Hewitt GM. (1996) Some genetic consequences of Ice Ages, and their role in divergence and speciation. Biol J Linn Soc 58:247–76.[CrossRef]
Hewitt GM. (1999) Post-glacial re-colonization of European biota. Biol J Linn Soc 68:87–112.[CrossRef][Web of Science]
Hewitt GM. (2000) The genetic legacy of the Quaternary Ice Ages. Nature 405:907–13.[CrossRef]
Hewitt GM. (2004) Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond Ser B Biol Sci 359:183–95.
Irwin DE, Bensch S, Price TD. (2001) Speciation in a ring. Nature 409:333–7.[CrossRef][Medline]
Ivankina EV, Kerimov AB, Formozov NA. (1997) Song variability and the problem of the "ring of races" in the great tit (Parus major). Byull Mosk O-va Ispyt Prir Otd Biol 102:13–9 [in Russian].
Kerimov AB and Formozov NA. (1986) Zones of secondary contacts in ring range of the great tit (south-western Turkmenia. Priamur'e). Bull Moscow Soc Naturalists27–31 [in Russian].
Kvist L, Martens J, Ahola A, Orell M. (2001) Phylogeography of a Palearctic sedentary passerine, the willow tit (Parus montanus). J Evol Biol 14:930–41.[CrossRef]
Kvist L, Martens J, Higuchi H, Nazarenko AA, Valchuk OP, Orell M. (2003) Evolution and genetic structure of the great tit (Parus major) complex. Proc R Soc Lond B Biol Sci 270:1447–54.[Medline]
Kvist L, Ruokonen M, Lumme J, Orell M. (1999) The colonization history and present-day population structure of the European great tit (Parus major major). Heredity 82:495–502.
Kvist L, Ruokonen M, Thessing A, Lumme J, Orell M. (1998) Mitochondrial control region polymorphism reveal high amount of gene flow in Fennoscandian willow tit (Parus montanus borealis). Hereditas 128:133–43.[CrossRef][Web of Science][Medline]
Liebers D, Helbig AJ, De Knijff P. (2001) Genetic differentiation and phylogeography of gulls in the Larus cachinnans–fuscus group (Aves: Charadriiformes). Mol Ecol 10:2447–62.[CrossRef][Medline]
Longmire L, Maltbie M, Baker RJ. (1997) Use of "lysis buffer" in DNA isolation and its implication for museum collections. Occasional Papers OP-163 (Museum of Texas Tech University, Lubbock, Texas).
Nazarenko AA, Valchuk OP, Martens J. (1999) Secondary contact and overlap of Parus major and P. minor populations in the middle Amur river basin. Zool Zhurnal 78:372–81.
Nei M. (1987) Molecular evolutionary genetics (Columbia University Press, New York).
Pavlova A. (2004) Comparative phylogeography of Eurasian birds [PhD dissertation] (University of Minnesota, St Paul, MN).
Pavlova A, Zink RM, Drovetski SV, Red'kin Ya, Rohwer S. (2003) Phylogeographic patterns in Motacilla flava and Motacilla citreola: species limits and population history. Auk 120:744–58.[CrossRef]
Pavlova A, Zink RM, Rohwer S. (2005) Evolutionary history, population genetics and gene flow in the common rosefinch (Carpodacus erythrinus). Mol Phylogenet Evol 36:669–81.[CrossRef][Web of Science][Medline]
Pavlova A, Zink RM, Rohwer S, Koblik EA, Red'kin YA, Fadeev IV, Nesterov EV. (2005) Mitochondrial DNA and plumage evolution in white wagtails. J Avian Biol 36:322–36.[CrossRef]
Posada D and Crandall KA. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–8.
Posada D and Crandall KA. (2001) Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16:37–45.[CrossRef][Medline]
Postma E and van Noordwijk AJ. (2005) Gene flow maintains a large genetic difference in clutch size at a small spatial scale. Nature 433:65–8.[CrossRef][Medline]
Ramos-Onsins SE and Rozas J. (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–100.
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–7.
Ruokonen M and Kvist L. (2002) Structure and evolution of the avian mitochondrial control region. Mol Phylogenet Evol 23:422–32.[CrossRef][Web of Science][Medline]
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Ehrlich HA. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–91.
Salzburger W, Martens J, Nazarenko AA, Sun Y-H, Dallinger R, Sturmbauer C. (2002) Phylogeography of the Eurasian willow tit (Parus montanus) based on DNA sequences of the mitochondrial cytochrome b gene. Mol Phylogenet Evol 24:26–34.[CrossRef][Web of Science][Medline]
Schneider S and Excoffier L. (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1070–89.
Schneider S, Roessli D, Excoffier L. (2000) Arlequin: a software for population genetic data analysis. Version 2.000. (Genetics and Biometry laboratory, University of Geneva, Geneva, Switzerland) Available from: http://lgb.unige.ch/arlequin/. Accessed 2005 Feb 24.
Smirenskiy SM. (1986) Ecological-geographic analysis of avifauna of Middle Priamur'e [Avtoreferat of the PhD dissertation] (Moscow State University [in Russian], Moscow, Russia).
Stepanyan LS. (2003) Conspectus of the ornithological fauna of Russia and adjacent territories (within the borders of the USSR as a historic region) (Academkniga, Moscow, Russia).
Swofford DL. (2000) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b2 (Sinauer, Sunderland, MA).
Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF. (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453–64.[CrossRef][Medline]
Tajima F. (1989) The effect of change in population size on DNA polymorphism. Genetics 123:597–601.
Tajima F. (1996) The amount of DNA polymorphism maintained in finite population when the neutral mutation rate varies among sites. Genetics 143:1457–65.[Abstract]
Tamura K and Nei M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–26.[Abstract]
Tarasov PE, Peyron O, Guiot J, Brewer S, Volkova VS, Bezusko LG, Dorofeyuk NI, Kvavadze EV, Osipova IM, Panova NK. (1999) Last glacial maximum climate of the former Soviet Union and Mongolia reconstructed from pollen and plant macrofossil data. Clim Dyn 15:227–40.
Verhulst S, Perrins CM, Riddington R. (1997) Natal dispersal of great tits in patchy environment. Ecology 78:864–72.[CrossRef][Web of Science]
Zhang D-X and Hewitt GM. (1996) Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol Evol 11:247–51.[CrossRef]
Zink RM. (2005) Natural selection on mitochondrial DNA in Parus and its relevance for phylogeographic studies. Proc R Soc Lond B Biol Sci 272:71–8.[CrossRef][Medline]
Zink RM, Drovetski SV, Questiau S, Fadeev IV, Nesterov EV, Westberg MC, Rohwer S. (2003) Recent evolutionary history of the bluethroat (Luscinia svecica) across Eurasia. Mol Ecol 12:3069–75.
Zink RM, Drovetski S, Rohwer S. (2002) Phylogeographic patterns in the great spotted woodpecker (Dendrocopos major) across Eurasia. J Avian Biol 35:175–8.
Zink RM, Rohwer S, Drovetski S, Blackwell-Rago RC, Farrell SL. (2002) Holarctic phylogeography and species limits of three-toed woodpeckers. Condor 104:167–70.[CrossRef]
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