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Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea
Abstract
Variation and geographic differentiation in mitochondrial DNA (mtDNA) was studied in the widespread and phenotypically variable Eurasian nuthatch (Sitta europaea). To assess whether sequences were evolving in a selectively neutral fashion, we used McDonald-Kreitman [Nature 351 (1991) 652] tests and a tree-based method, which suggested that although ND2 sequences are affected by natural selection against slightly deleterious alleles, the effects do not compromise phylogeographic inferences. Three phylogenetic species-level clades of nuthatches were discovered, corresponding to the Caucasus, southern Europe, and northern Europe plus Asia. Unimodal mismatch distributions within each clade suggest that populations have undergone recent growth. A westward range expansion was inferred from the geographic pattern in nucleotide diversity. Although samples were insufficient, it is possible that nuthatches in England and Japan are recently differentiated. Two specimens of the subspecies S. e. arctica formed a sister group to all other S. europaea, differing by ca. 10% uncorrected sequence divergence, pointing the need for additional study of this phenotypically distinct taxon. As with other species, mtDNA data support major phenotypic distinctions, but not subspecies.
... Traditionally, the form arctica has been treated conspecific with S. europaea (vaurie, 1959;harrap & Quinn, 1996;harrap, 2008) and was included as one of its subspecies by some authors until recently (clements et al., 2017). However, because of strong evidence of its genetic distinctiveness against S. europaea (Zink et al., 2006;hunG et al., 2012), S. arctica has been recently upgraded to species level by several taxonomic authorities (Dickinson & christiDis, 2014;Del hoyo & collar, 2016;Gill et al., 2020). Recent findings have suggested that S. arctica is only distantly related to a monophyletic group of S. europaea, S. cashmirensis, and S. nagaensis; however, its phylogenetic relationships to these species and to S. himalayensis were not well resolved (chen et al., 2019). ...
... Among-island diversification was found in the sulphur-billed nuthatch, S. oe nochlamys, from the Philippines (campbell et al., 2016). Furthermore, in the Palearctic substantial intraspecific differentiation was found in the Eurasian nuthatch, S. eu ropaea, with three major genetic lineages to be distinguished in (i) the Western Palearctic, (ii) the Eastern Palearctic, and (iii) in the Caucasus (Zink et al., 2006;hunG et al., 2012). Recent studies identified two further Caspian mitochondrial lineages of S. europaea from Iran (naZariZaDeh et al., 2016) and another distinct Chinese lineage including the subspecies S. e. sinensis and S. e. formosana (chen et al., 2019). ...
... Marker choice: We amplified and sequenced the three markers used by pasQuet et al. (2014) for optimal comparison with their multi-locus data set: two mitochondrial genes (cytochrome b [cyt b] and cytochrome oxidase subunit I [COI]) and the nuclear RAG1. In addition, we sequenced the mitochondrial NADH dehydrogenase subunit 2 (ND2) for comparison with the data set by Zink et al. (2006) for S. europaea, and a further nuclear marker, intron 2 of the nuclear myoglobin gene (myo). ...
Nuthatches of the Holarctic and partly Indo-Malayan genus Sitta have been subject to a number of phylogenetic analyses; however, the most complete phylogenetic hypothesis to date missed several Asian species-level taxa, was based on a limited sampling, and included only one sample per species. Other recent studies were mainly focused on phylogeographic patterns of single Asian species but failed to unam-biguously resolve their phylogenetic relationships. In this study, we provide a time-calibrated multi-locus phylogeny of nuthatches (Sitta) including 27 out of 28 currently recognized species. To account for intraspecific variation we included a number of subspecific taxa in our sampling, e.g. for the phenotypically diverse Eurasian nuthatch, S. europaea. Within the latter species (our clade X) three phenotypically distinct phylogroups started diversifying from the early Pleistocene on: (i) brown-bellied forms of the sinensis group from China and Tai-wan with smallest body size dimensions, (ii) white-bellied forms of the Central and Eastern Palearctic europaea group with average body size dimensions, and (iii) brown-bellied forms of the Western Palearctic and Caucasian caesia group with largest body size dimensions. The three phylogroups are connected by chains of phenotypically intermediate populations in Eastern Europe (e.g. ssp. homeyeri) and in Far East Russia and northeastern China (ssp. amurensis). The Eurasian nuthatch was sister to a monophyletic clade IX comprising five Sino-Himalayan species: S. nagaensis, S. cashmirensis, S. castanea, S. neglecta, and S. cinnamoventris. In the Sino-Himalayas, ecological segregation along the elevational gradient was established from the mid-Miocene onset of nuthatch diversification until the recent ecological segregation among chestnut-bellied forms of the S. castanea complex during the Pleistocene.
... The Eurasian Nuthatch is categorized into three groups according to its morphological characteristics: caesia (Western Europe, North Africa, Asia Minor, the Caucasus, and Iran), europaea (Scandinavia to Japan, south to the eastern Tien Shan Mountains, northern China) and sinensis (central and eastern China) (Harrap & Quinn, 1995). In a recent mtDNA-based study, Zink, Drovetski, and Rohwer (2006) revealed three major clades for S. europaea: (i) the Caucasus, (ii) western Eurasia (United Kingdom, Switzerland and western Russia), and (iii) eastern/northwestern Eurasia (northern Europe and Asia). Similarly, a study by Hung, Drovetski, and Zink (2012) based on ND2 sequences plus 13 introns confirmed that the three haplogroups (Asian, European, and Caucasian) became separated over a short time span (Zink et al., 2006;Hung et al., 2012). ...
... In a recent mtDNA-based study, Zink, Drovetski, and Rohwer (2006) revealed three major clades for S. europaea: (i) the Caucasus, (ii) western Eurasia (United Kingdom, Switzerland and western Russia), and (iii) eastern/northwestern Eurasia (northern Europe and Asia). Similarly, a study by Hung, Drovetski, and Zink (2012) based on ND2 sequences plus 13 introns confirmed that the three haplogroups (Asian, European, and Caucasian) became separated over a short time span (Zink et al., 2006;Hung et al., 2012). ...
... The Eurasian Nuthatch in Iran is represented by two subspecies, namely S. e. rubiginosa (Tschusi-Schmidhoffen, 1905) and S. e. persica (Witherby, 1903) in the Alborz and Zagros forested mountains, respectively (Kaboli et al., 2012). Previous studies (Hung et al., 2012;Zink et al., 2006) have not taken into account the Nuthatches of Iran and this study was designed to determine the phylogenetic status and conservation units of Eurasian Nuthatches. ...
The Eurasian Nuthatch (Sitta europaea Linnaeus, 1758) is a resident bird in the Alborz and Zagros deciduous forests. We investigated the phylogenetic relationships and the taxonomic position of the Eurasian Nuthatch among other separated lineages of Eurasia with the help of blood samples collected from 19 individuals belonging to four populations in the Eastern and Western Alborz, as well as in the Northern and Southern Zagros forests. Genetic variation was then analysed using complete ND2 gene sequence (1041 bp) and phylogenetic analysis was done using Bayesian and maximum likelihood inference. Additionally, a median-joining algorithm was used to reveal the relationships among haplotypes. The results of the phylogenetic and haplo-type network analyses indicated that Eurasian Nuthatch haplotypes from the Alborz and Zagros Mountains form lineages distinct from the Asian, Caucasian and European haplotypes. Furthermore, an analysis of molecular variance (AMOVA) detected significant (P<0.001) genetic structure among the lineages. The Asian, European, Caucasian and Alborz lineages diverged from one another by an uncorrected genetic distance ranging from 0.029 to 0.039, while the Zagros lineage showed a slightly lower genetic divergence from the Caucasian lineage (0.006), but it did not share any haplotype with the Caucasian lineage. Thus, we suggest considering five Conservation Significant Units (CSU) for the Eurasian Nuthatches as the result of used dataset.
... In addition, the Caucasus, which include a high percentage of endemic subspecies and differentiated populations (Stepanyan 2003), is believed to have become a remote forest island 430,000 years ago based on paleontological and paleoclimatic evidence (see Tyrberg 1998;EPICA 2004). Several published mtDNA phylogeographic studies of widespread species do not support a common pattern across the Palearctic, suggesting idiosyncratic evolutionary histories (e.g., Drovetski et al. 2004;Hewitt 2004;Zink 2005;Zink et al. 2006Haring et al. 2007;Fedorov et al. 2008). However, it is possible that the inconsistent patterns of mtDNA differentiation among species simply reflect variance in the coalescence process or the effects of natural selection-that is, biases that can affect any single locus. ...
... It is an obligate forest species and therefore provides an example of how the Palearctic forest fauna responded to historical climate changes. A mtDNAbased study revealed three distinct haplogroups generally corresponding to the Asia (although Finland and Vyatka are located in Europe, we grouped them with the Asian group for convenience), Europe, and Caucasus ( Fig. 1; Zink et al. 2006). However, the evolutionary relationships among these three phylogroups were unresolved and appeared to be a trichotomy. ...
... However, the evolutionary relationships among these three phylogroups were unresolved and appeared to be a trichotomy. Zink et al. (2006) detected selection against slightly deleterious alleles in the ND2 sequences of nuthatches but argued that its effect on phylogeographic inference was negligible. In this study, we (1) test whether selection acts on mtDNA or nuclear loci and obscures historical inference, (2) examine whether nuclear genes recover the three mtDNA phylogroups and whether multilocus species trees clarify their relationship, and (3) compare multilocus estimates of gene flow and population history with those from mtDNA. ...
Our understanding of species phylogeography in much of the Palearctic is incomplete. In addition, many existing studies based solely on mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic history because of the effects of lineage sorting, natural selection, or hybridization. We analyzed 13 introns to assess a mtDNA study of the Eurasian nuthatch (Sitta europaea) that suggested a seemingly contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia. Neutrality tests showed no evidence of selection on either the mtDNA or nuclear sequences. Most nuclear gene trees, except for Z-linked ones, did not recover the three lineages, which we attribute to recent splitting. Analyses of the 13 introns combined revealed the same three groups as did the mtDNA and suggested that nuthatches experienced a trichotomous (or two indistinguishable) split(s) 1-2 million years ago (Mya) and have remained isolated with trifling if not zero gene flow since then, and the Asian group increased in population size. This result demonstrates the usefulness of mtDNA in discovering phylogeographic patterns. The use of multiple nuclear loci facilitated detection of an introgressed individual and improved estimates of process parameters such as divergence time and population expansion. We recommend that phylogeographic studies should be based on both mtDNA and nuclear genes.
... These patterns raise an intriguing question: why Armenian hoopoes exhibited similar mtDNA sequences to European hoopoes, while showing different genotypes in microsatellites? Indeed, this is not the first investigation showing that Caucasian birds have complex biogeographic histories (Zink et al., 2006). Caucasian endemic haplotypes have been reported in several species, for instance, the European nuthatch (Zink et al., 2006), the Winter wren (Drovetski et al., 2004), and the White wagtail (Pavlova et al., 2003). ...
... Indeed, this is not the first investigation showing that Caucasian birds have complex biogeographic histories (Zink et al., 2006). Caucasian endemic haplotypes have been reported in several species, for instance, the European nuthatch (Zink et al., 2006), the Winter wren (Drovetski et al., 2004), and the White wagtail (Pavlova et al., 2003). Previous research suggested that some sedentary Caucasian birds recently diverged from European populations which has been proved by mtDNA markers (Drovetski et al., 2004). ...
The Hoopoe (Upupa epops epops) breeds widely in Eurasia and most populations migrate to Africa during the boreal winter. To date, data regarding its phylogeography in Europe are missing. In this study, we investigated the phylogeography and population genetics of Hoopoes by means of mitochondrial DNA (mtDNA) sequencing as well as microsatellite genotyping. Our analyses revealed 32 haplotypes in the cytochrome c oxidase subunit I (COI) (269 individuals) and 50 haplotypes in cytochrome b (cyt b) (233 individuals). Analyses of mtDNA clearly demonstrated that the bulk of variance (98.23%) could be attributed to inner-population variance. Thus, the low frequency single nucleotide substitutions resulted in “star-like” haplotype networks without define geographical structure. Hoopoes clearly experienced a bottleneck followed by sudden expansion, as was also apparent from tests on the unimodal mismatch, Bayesian skyline plot, significant negative neutrality tests as well as bottleneck signals. These tests pointed to strong demographic fluctuations in the hoopoe populations. GENELAND, DAPC and STRUCTURE analyses of microsatellites along with their corresponding Fst values suggested that current genetic restriction separates birds from Armenia from the remaining populations. Except for hoopoes from Armenia, all the European populations exhibited an admixed phylogeographic pattern. We conclude that this genetic panmixia might be a consequence of a combination of historical events (e.g. repeated colonizations and retreatments from northern habitats during the Pleistocene and a sudden postglacial expansion) and current processes (e.g. long-distance migration, immigration or population recruitments).
... For several vertebrates and invertebrates the Carpathians have been identified as a refugia during the LGM (Jaarola and Searle, 2002;Deffontaine et al., 2005;Ursenbacher et al., 2006;Wójcik et al. 2010;Homburg et al., 2013), as have areas in the vicinity of the Alps (e.g., Deffontaine et al., 2005;Ursenbacher et al., 2006;Schmitt et al., 2007). Southern Siberia, the Urals, the hills of the Crimea and Caucasus have also been suggested (reviewed by Zink et al., 2006;Bogdano wicz et al., 2009), and several cryptic refugia in north western Europe have been hypothesised in areas with suitable stable microclimates (see Stewart andLister, 2001 andBhagwat et al., 2008). ...
... We suggest that the data in our study present a scenario of ice-age survival and subsequent recolonisation of P. pipistrellus s.str. in both multiple refugia within the Mediterranean peninsulas, and potentially in extra-Mediterranean refugia in both eastern and western Europe. It seems likely that a northern refugia existed for this species in the region of the Caucasus and Black Sea, an area described to harbour distinct genetic lineages in other continental species, for example the root vole Microtus oeconomus (Brunhoff et al., 2003), the Eurasian nuthatch Sitta europaea (Zink et al., 2006), Myotis bechsteinii (Kerth et al., 2008). ...
The geographic ranges of European plants and animals underwent periods of contraction and re-colonisation during the climatic oscillations of the Pleistocene. The southern Mediterranean peninsulas (Iberian, Italian and Balkan) have been considered the most likely refugia for temperate/warm adapted species. Recent studies however have revealed the existence of extra-Mediterranean refugia, including the existence of cryptic north-west European refugia during the Last Glacial Maxima (24–14.6 kyr BP). In this study we elucidated the phylogeographic history of two sibling bat species, Pipistrellus pipistrellus and P. pygmaeus in their western European range. We sequenced the highly variable mtDNA D-loop for 167 samples of P. pipistrellus (n = 99) and P. pygmaeus (n = 68) and combined our data with published sequences from 331 individuals. Using phylogenetic methodologies we assessed their biogeographic history. Our data support a single eastern European origin for populations of P. pygmaeus s.str., yet multiple splits and origins for populations of P. pipistrellus s.str., including evidence for refugia within refugia and potential cryptic refugia in north western Europe and in the Caucasus. This complex pattern in the distribution of mtDNA haplotypes supports a long history for P. pipistrellus s.str. in Europe, and the hypothesis that species with a broad ecological niche may have adapted and survived outside southern peninsula throughout the LGM.
... Recent studies have shown that the northeast Siberian form arctica differs from other populations of Sitta europaea in plumage, size and proportions (Red'kin & Konovalova 2006), vocalizations (Leonovich et al. 1996) and mtDNA sequences (10% sequence divergence in ND2, Zink et al. 2006). The two groups have overlapping ranges in eastern Siberia, but only one putative intermediate specimen has been reported in the literature and no further intermediates were located in museums (Red'kin & Konovalova 2006). ...
... • Sitta arctica Siberian Nuthatch (monotypic) • Sitta europaea Eurasian Nuthatch (polytypic) Phylogeographical analyses (Zink et al. 2006, Hung et al. 2012) and reports of reduced intro-gression in contact zones (Red'kin & Konovalova 2006) indicate that Eurasian Nuthatch may include additional species but further study is necessary. ...
... For PCR amplification of the mitochondrial protein-coding gene, NADH dehydrogenase subunit two (ND2), we used the following primers: L5204 (Tello and Bates 2007); H6312 (Cicero and Johnson 2001); L5219 and H6313 (Sorenson et al. 1999). The ND2 gene is widely used in avian phylogeographic studies (Zink et al. 2006, Miller et al. 2008, Fernandes et al. 2012, Ritter et al. 2021 and there is strong indication that most mtDNA results can be taken as reliable indicators of population structure, phylogeographic patterns, and species limits (Zink and Barrowclough 2008). ...
We examined phylogeographic patterns and cryptic diversity within the royal flycatcher, Onychorhynchus coronatus (Aves: Onychorhynchidae), a widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of the six recognized subspecies was constructed from mtDNA sequence data of the NADH dehydrogenase subunit two gene, using Bayesian Inference and Maximum Likelihood methods. Phylogenetic analyses revealed high levels of intraspecific divergence within O. coronatus, supporting the existence of at least six independent lineages. The phylogenetic results uncovered the following relationships: (O. c. swainsoni [Southern Atlantic Forest], (O. c. coronatus [western Amazonia], (O. c. castelnaui [eastern Amazonia], (O. c. mexicanus [Central America], (O. c. occidentalis [Tumbesian], O. c. fraterculus [extreme northwestern South America])))). Biogeographic and dating analyses suggest that vicariant and dispersal events acted across approximately six million years to influence lineage diversification within this genus. Some of those events include the formation of the Amazon River and its tributaries, Andean uplift, and climatically induced vegetational shifts. Phylogenetic and biogeographic analyses of O. coronatus lineages support a hypothesis of area relationships in which the first divergence event isolated the Southern Atlantic Forest from Amazonia during the Late Miocene/Early Pliocene. This event was followed by the split of western and eastern Amazonia at the Early/Late Pliocene, the divergence of cis‐ and trans‐Andean lowland regions also at the Early/Late Pliocene, the split between Central America and the extreme northwestern South America/Tumbes at the Early/Middle Pleistocene, and the split between extreme northwestern South America and Tumbes at Middle/Late Pleistocene. Subsequent divergence of the southern and northern populations in the western and eastern Onychorhynchus lineages took place during the Pleistocene. Comparison of phylogenetic trees and patterns in Onychorhynchus with those from published work suggests that across large New World radiations such as the Suboscines, some co‐distributed lineages began to diverge long before others, which exemplifies the complexity of their evolutionary history.
... Entre los genes mitocondriales más comúnmente empelados en filogeografía están la subunidad 2 Deshidrogenasa NADH (ND2) y citocromo b, estos son marcadores moleculares muy conocido y empelados en estudios filogenéticos de aves, han aportado mucha información gracias a su dicha neutralidad evolutiva (Zink et al. 2006) y ritmo constante de evolución (Moore, W.S., DeFilippis 1997;Avise 2000). (Moore, W.S., DeFilippis 1997;Avise 2000). ...
El estudio filogeográfico ha documentado que los eventos geológicos del Plioceno junto a los ciclos glaciares del Cuaternario, tuvieron un papel muy importante en la diversificación biológica de Norteamérica. La especie Myioborus miniatus habita desde el norte de México hasta Argentina, tiene un registro de 12 subespecies a partir de diferencias morfológicas.
Un estudio filogeográfico relacionó la variación genética subespecífica con la discontinuidad del hábitat y cambios climáticos durante el Pleistoceno Tardío. Sin embargo, no se integró a la subespecie Myioborus miniatus miniatus. Este trabajo se plantea como propósito deducir el patrón filogeográfico de la subespecie Myioborus miniatus miniatus.
A partir de la obtención de 62 secuencias del gen mitocondrial ND2, se realizó un árbol filogenético bayesiano, una red de haplotipos y se obtuvieron los índices de diversidad genética y valores de FST entre las poblaciones. La historia demográfica fue descrita con
los índices D de Tajima, F de Fu y valor de regardness, el valor de Tau permitió calcular el tiempo desde que comenzó la expansión. Por último, el tamaño efectivo de la población a través del tiempo fue graficado por medio de un análisis bayesiano Skyline Plot.
El análisis filogenético, que incluye todas las subespecies de Myioborus miniatus, indico que M. miniatus miniatus se encuentra en el linaje basal, además, este presenta un nodo bien soportado pero sin monófilia. . La diversidad genética presento un valor alto (0.8909) mientras que la diversidad nucleotidica promedio fue de 0.00191. El análisis de genética de poblaciones indica que no hay estructura genética. En cuanto a la historia demográfica,
el análisis Skyline Plot y pruebas de neutralidad indican un escenario de expansión demográfica. A su vez las pruebas de distribución mismatch indican un cambio súbito en el tamaño de la población. En conjunto los resultados indican un incremento del tamaño efectivo de la población durante el último máximo glaciar hace 60 mil años.
... O mtDNA apresenta características desejáveis para estudos filogeográficos, como a ausência de recombinação gênica e rearranjos genéticos, baixa taxa de mutação e herança uniparental (Bock 2007), sendo muito utilizado em estudos com animais (Zink et al. 2006). Nas plantas, o mtDNA é compacto, denso, conservado e pouco informativo quando comparado ao cpDNA (Dambrostka & Qiu 2004). ...
Overall, the aim of this study was to characterize the population dynamics and understand the phylogeographic scenario of the conifer Podocarpus lambertii in order to generate knowledge to promote its conservation over time.
... An alternative dividing line within wide-ranging Palaearctic species has been proposed further west in the Central Palaearctic 27,28,38,39 . In other studies, Palaearctic populations have also been characterized by divisions into multiple clusters corresponding to glacial refugia during the Last Glacial Maximum (LGM) 40,41 . Conversely, some wide-ranging species lack or show only shallow population structure despite the vast geographical area involved 9,25,28,31,[42][43][44] . ...
Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.
... (Harrap, 2008), a i haplotipovi filogenetske linije corsa/caucasica nisu prisutni bilo gde na području južne Evrope. Treća hipoteza uključuje pozitivnu selekciju mitohondrijalne DNK kao kod srodne vrste brgljeza (Sitta europaea) (Zink, Drovetski and Rohwer, 2006) što bi značilo da je mitohondrijalna filogenetska linija corsa/caucasica nije neutralno evoluirala. Mada u raspoloživim podacima nije dobijen dokaz o pozitivnoj selekciji koristeći MK testove, više uzoraka i statističkih analiza je potrebno da bi se ova hipoteza odbacila (Garvin et al., 2015). ...
... The ENMs of southern 39 lineages tended to cross-predict with their neighboring lineages whereas those of northern Table S1). We obtained 230 ND2 sequences, including 47 samples from mainland 109 China and Taiwan (i.e., East Asia) sequenced for this study and 183 samples from North 110 Asia, Europe, Caucasus and Iran sequenced for our previous studies (Hung et al., 2012;111 Nazarizadeh et al., 2016;Zink et al., 2006) or downloaded from the GenBank (Table S1). (Table S1). ...
Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche‐mediated evolution may differ among climatic regimes, and thus species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (1) how many lineages have evolved across the continent‐wide range of the Eurasian nuthatch (Sitta europaea), (2) whether the lineages’ niches are significantly divergent or conserved, and (3) how their niche evolution explains their geographic distribution. Phylogenetic reconstruction and ecological niche models (ENMs) showed that the Eurasian nuthatch contained six parapatric lineages that diverged within two million years and did not share identical climatic niches. However, the niche discrepancy between these distinct lineages was relatively conserved compared with the environmental differences between their ranges and thus was unlikely to drive lineage divergence. The ENMs of southern lineages tended to cross‐predict with their neighboring lineages whereas those of northern lineages generally matched with their abutting ranges. The coalescence‐based analyses revealed more stable populations for the southern lineages than the northern ones during the last glaciation cycle. In contrast to the overlapping ENMs, the smaller parapatric distribution suggests that the southern lineages might have experienced competitive exclusion to prevent them from becoming sympatric. On the other hand, the northern lineages have expanded their ranges and their current abutting distribution might have resulted from lineages adapting to different climatic conditions in allopatry. This study suggests that niche evolution may affect lineage distribution in different ways across latitude.
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... This climate shift had a strong effect on distribution and diversification patterns of biota particularly in the Northern hemisphere (Head & Gibbard, 2005). Similar splits are often found between endemic bird lineages of the Caucasus and their European counterparts with the Caucasus being considered as an important Pleistocene forest refugium (Drovetski, 2003;Drovetski et al., 2004;Hung et al., 2017;Hung, Drovetski, & Zink, 2012Zink, Drovetski, & Rohwer, 2006). Divergence estimates between Caucasian and European populations of 30 forest-dwelling avian species ranged from 0-1.7 Ma with residents, habitat specialists, and species with low effective population sizes being more differentiated than migrants, habitat generalists and abundant species (Hung et al., 2017). ...
opulation divergence could be strongly affected by species’ ecology and might not be a direct response to climate‐driven environmental change. We tested this in the middle spotted woodpecker (Dendrocoptes medius), a non‐migratory, low‐dispersal habitat specialist associated with old deciduous forests of the Western Palearctic. We present the first phylogeographic study of this species integrating genetic data (three mitochondrial loci, one autosomal and one Z‐linked intron) with species distribution modelling. Based on this species’ ecology, we predicted that the middle spotted woodpecker could have colonized its current range from multiple Last Glacial Maximum (LGM) refugia and that strongly structured populations could be expected. Indeed, we discovered a strong genetic divergence between Asian and European populations, with a split estimated at around one million of years ago. This was surprising given only slight intraspecific variation in plumage and morphology. Although there was no significant phylogeographic structure within the Asian and European groups, we cannot exclude the possibility of multiple refugia within either group during the LGM. This has to be further investigated with more extensive geographic sampling and larger number of variable independently evolving markers. Future studies should also investigate potential differences in vocalizations and ecology between the two groups. Lineages showing similar level of genetic differentiation including woodpeckers are often treated as species‐level taxa. Comparison of our results with the phylogeographic history of other woodpeckers, suggests that sympatric species with similar life‐histories might have idiosyncratic phylogeographic patterns probably resulting from different ecological requirements or historic stochasticity.
... This in itself was not a surprising discovery, as molecular characters frequently reveal divergent taxa embedded within traditionally recognized species. This is especially true for those species with extensive phenotypic variation or large Holarctic or Palearctic ranges, e.g. the former winter wren that is currently treated as three distinct species (Troglodytes troglodytes, T. hiemalis, and T. pacificus; Drovetski et al., 2004), the Eurasian nuthatch Sitta europaea (Zink et al., 2006;Hung et al., 2012), or the horned lark Eremophila alpestris (Drovetski et al., 2014). In fact, based on its extensive phenotypic variation (see e.g., deo Hoyo et al., 2004), some taxonomists have suggested that the yellow wagtail complex consists of four (Stepanyan, 2003) or as many as eleven (Sangster et al., 1998;Sangster et al., 1999) closely related species. ...
... Auf die Eigenart der Rufe von Sitta arctica verwiesen L. A. Portenko (1939) sowie V. V. Leonovič et al. (1996). Die Analyse der mitochondrialen DNA (vor allem des Gens ND2, 1041 n.p.) zeigte, dass Sitta arctica weit entfernt von allen Gruppierungen der Formen von Sitta europaea sensu lato steht (Zink et al. 2006 E. Mayr (1956) charakterisierte die individuelle und geografische Variation der Vertreter eines der "Problem-Komplexe", der Schafstelzen Motacilla flava sensu lato, als rätselhaft und nebulös, am "Schwindel erregendsten" in der gesamten paläarktischen Avifauna. Die Uneinigkeit der Wissenschaftler bezog sich vor allem auf die Anzahl der anerkannten Taxa, ihre Verbreitung und den Charakter ihrer Wechselbeziehungen in den Kontaktzonen. ...
Species or not? Contentious taxonomic opinions on the birds of North Eurasia
The article presents the position of the leading Russian taxonomists in the current discussion of the
category ‘species’, as well as the biological and phylogenetic species concept (BSC, PSC). This alternative
draft concept differs significantly from the standpoint of West and Central European taxonomists,
in that it does not endorse the primacy of PSC and the extremely forced division of species, but rather
encourages the application of morphological, phylogenetic, biological, ecological and bioacoustic criteria
for every status identification of a taxon. It is possible - in the case of inadequate material for many
taxa - to apply temporary and interim solutions, such as superspecies and semispecies, in order to arrive
at a compromise between reflecting the real family relationships and the practicability of nomenclature.
Taxonomy today is trapped in a crisis because of its discontinuity, and its departure from its
proper task - the hierarchical structure of the nomenclature.
The opinions of the authors are presented and discussed using a number of examples (Great Egret,
Water Rail, Herring Gull, Great Grey Shrike, Western Yellow Wagtail, European Stonechat, Great Reed
Warbler, Eurasian Nuthatch, Arctic Warbler, Golden Oriole).
... Rozpoznanie czynników odpowiedzialnych za spadek liczebności gatunku wymaga pilnych badań i adekwatnych działań ochronnych. (Zink et al. 2006). ...
... Red'kin & Konovalova (2006) indicated that the range of arctica "borders and even partly overlaps with the ranges of three subspecies of S. europaea", but their map depicts an extensive area of sympatry with S. e. baicalensis, which is either conclusive evidence of two species or an indication of considerable winter intermingling. However, limited mitochondrial DNA sampling of arctica shows strong divergence from all other S. europaea forms (Zink et al. 2006). ...
... Fluctuations in population size reflect the idiosyncratic life-history characteristics of a given population, but concordant demographic fluctuations among species could also reflect long-term trends in environmental conditions. Many studies have considered the historical demography of a single species with a single marker (usually mtDNA, Merilä et al. 1997, Zink et al. 2006, Hawley et al. 2008, Lerner et al. 2009, Norgate et al. 2009, Brace et al. 2012). More recently, authors have used multiple markers to study individual species (Firestone et al. 1999, Tchaicka et al. 2007, Bos et al. 2008, Reding et al. 2010, Nietlisbach et al. 2012. ...
Molecular markers can be used to infer the demographic history of a given species, but many historic processes simultaneously impact multiple species. Thus, comparative historical demography has the potential to provide insight into drivers of evolution. In this study, we used nuclear DNA (nDNA) sequences to corroborate (or refute) demographic inferences based on earlier mitochondrial DNA (mtDNA) data from 16 species of Hispaniola birds. Our previously published analysis suggested population expansion in five of six migratory species (following glacial retreat in North America), with less evidence of expansion in non-migratory species. Additional molecular markers should reduce locus-specific bias, and so we generated sequence data for several nuclear loci. Test statistics associated with the nDNA provided only equivocal evidence for population expansion in 10 of the 16 species. Discordance between mtDNA and nDNA is not uncommon because the two genomes are exposed to different selective pressures and have different effective population sizes and modes of inheritance. The nDNA analyses reported here cast some doubt on our earlier mtDNA inferences. They also suggest that the signal to noise ratio of demographic statistics is typically low because of the inherent variability in selective regimes and coalescence across loci.
... ND2 polymorphism in zebra finches is comparable to previous reports of ND2 nucleotide diversity in other passerines (π = 0.003-0.007, Table 1) [72][73][74]. Interestingly, ND2 nucleotide variation is twice as high in the Timor subspecies (π = 0.007) as in the Australian subspecies (π = 0.003) ( Table 1). ...
Two subspecies of zebra finch, Taeniopygia guttata castanotis and T. g. guttata are native to Australia and the Lesser Sunda Islands, respectively. The Australian subspecies has been domesticated and is now an important model system for research. Both the Lesser Sundan subspecies and domesticated Australian zebra finches have undergone population bottlenecks in their history, and previous analyses using neutral markers have reported reduced neutral genetic diversity in these populations. Here we characterize patterns of variation in the third exon of the highly variable major histocompatibility complex (MHC) class I α chain. As a benchmark for neutral divergence, we also report the first mitochondrial NADH dehydrogenase 2 (ND2) sequences in this important model system.
Despite natural and human-mediated population bottlenecks, we find that high MHC class I polymorphism persists across all populations. As expected, we find higher levels of nucleotide diversity in the MHC locus relative to neutral loci, and strong evidence of positive selection acting on important residues forming the peptide-binding region (PBR). Clear population differentiation of MHC allele frequencies is also evident, and this may be due to adaptation to new habitats and associated pathogens and/or genetic drift. Whereas the MHC Class I locus shows broad haplotype sharing across populations, ND2 is the first locus surveyed to date to show reciprocal monophyly of the two subspecies.
Despite genetic bottlenecks and genetic drift, all surveyed zebra finch populations have maintained high MHC Class I diversity. The diversity at the MHC Class I locus in the Lesser Sundan subspecies contrasts sharply with the lack of diversity in previously examined neutral loci, and may thus be a result of selection acting to maintain polymorphism. Given uncertainty in historical population demography, however, it is difficult to rule out neutral processes in maintaining the observed diversity. The surveyed populations also differ in MHC Class I allele frequencies, and future studies are needed to assess whether these changes result in functional immune differences.
... Леонович с соавторами (Леонович и др., 1996). Анализ митохондриальной ДНК (в основном ген ND2, 1041 н.п.) показал, что S.arctica далеко отстоит от всех группировок форм Sitta europaea sensu lato (Zink et al., 2006). Изучение коллекционного материала, накопленного к началу XXI в., показало, что гнездовой ареал формы arctica соприкасается и частично перекрывается с ареалами 3-х подвидов обыкновенного поползня: в бассейне правых притоков Енисеяс S. eu. ...
Ya.A. Red’kin, V.Yu. Arkhipov, S.V. Volkov, A.A. Mosalov, E.A. Koblik.
Species or non species? Controversial taxonomic treatments of birds of Northern Eurasia
Following the biological species concept and taking in to account such
criteria for assignment species rank as 1) morphological segregation, 2) molecular
philogenetic data, 3) ecological, ethological and distribution characteristics,
4) reproductive relationships we analyzed 8 categories of taxons with ambiguous
species rank.
We treat Acrocephalus orientalis and Sitta arctica as cryptic species but
with big genetic differentiation. In complex closely related taxons of Motacilla
flavasensu lato and Lanius excubitor sensu lato we allocate western and eastern
polytypic forms which treated as independent species. As closely related forms with
morphological and genetic differentiation and sympatric zone we treat Casmerodius
albusand Casmerodius modestus. As alopatric pair of species with morphological
and genetic differentiation, we tread Rallus aquaticus and Rallus indicus and
Oriolus oriolus and Oriolus kundoo, the differences in vocalization between both
Oriolus species are described. The complex of Phylloscopus borealissensu lato is
one are not well investigated case yet. We treat Japanese taxon P. xantodrias as full
species, but Kamchatka’s form examinandus as subspecies of Ph. borealisbecause
the relationships of these forms are not clear yet and remind the same situation with
Ph. collybita abietinusand Ph. c. tristis. The most palearctic forms of «herring gull
complex» we treat as independent species including such as Larus michahellis,
L. armenicus, L. fuscus, L. heuglini, L. vegae, L. mongolicus. Taxonomic status the
gulls from the Taimyr peninsula requires further detailed investigation.
... The overall high diversity of mtDNA in natural populations suggests that selective sweeps are rare (Karl et al. 2012), with little evidence that selection has influenced patterns of mtDNA diversity in vertebrates (Nabholz et al. 2008(Nabholz et al. , 2009McCusker and Bentzen 2010). Selection does not appear to invalidate intraspecific phylogenetic inferences from mtDNA (Zink 2005, Kivisild et al. 2006, Zink et al. 2006). Lastly, numerous phylogeographic studies of birds have reported congruent histories between mitochondrial and nuclear genes (Hung et al. 2013 and references therein), which suggests that mtDNA phylogeographic patterns in most avian species are because of gene flow and genetic drift rather than natural selection (Drovetski et al. 2009;Hung et al. 2012Hung et al. , 2013Zink et al. 2013). ...
We conducted a phylogeographic study of the Gambel's Quail (Callipepla gambelii) using sequences of the mitochondrial control region and NADH dehydrogenase subunit 2 (ND2) obtained from 167 specimens including hunter–harvested wings and museum study skins. The Gambel's Quail exhibited strong phylogeographic structure, large genetic gaps, and relatively high levels of haplotype (Hd = 0.79) and nucleotide diversity (π = 0.01). Thirty-four Gambel's Quail haplotypes clustered into two distinct haplogroups, with two additional highly divergent haplotypes. Distribution of the haplogroups was not concordant with sampled subspecies or ecogeographic regions; however, the overall distribution of the two haplogroups suggests that the Gambel's Quail may have been isolated in separate refugia of the Chihuahuan and Sonoran deserts during the Pleistocene. Both haplogroups appear to have undergone recent demographic expansion, possibly related to climatic changes associated with the onset of drier conditions in southwestern North America following the end of the Last Glacial Maximum.
... We used two types of molecular data: DNA sequence from the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and amplified fragment length polymorphisms (AFLPs; Vos et al. 1995). ND2 is a well-known mtDNA marker in birds and has been shown to be particularly informative and approximately neutrally evolving (Zink et al. 2006), hence providing confidence when used to estimate population parameters (Lovette 2004). AFLPs have several benefits, including a sampling of the entire genome and inclusion of many unlinked loci. ...
Diversification during the Pleistocene is thought to have contributed significantly to taxonomic diversity at high latitudes. In some cases this diversity is cryptic, in that speciation has occurred with little change in phenotype. We examined the genetic signatures of one such case, between American and Pacific golden-plovers (Pluvialis dominica and P. fulva, respectively). This high-latitude species pair is morphologically very similar, and they are obligate long-distance migrants. They were only relatively recently recognized as separate species. We used 1,041 bp of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) from 20 dominica and 22 fulva and 242 amplified fragment length polymorphisms (AFLPs) from 29 individuals of each species sampled from sympatric and allopatric breeding populations to assess the levels of divergence, divergence date, and gene flow. A divergence date of ∼1.8 mya was estimated, and although we detected a seemingly old hybridization event, very little gene flow was detected (effectively zero). Significant genetic divergence was found between species (4.7% uncorrected sequence divergence in mtDNA; FST = 0.21 in AFLPs). We suggest that ecological factors and possibly sexual selection acted to limit gene flow during the divergence of these cryptic species during the Pleistocene, but given the age of the split we could not determine the mode of speciation that occurred.
... Rozpoznanie czynników odpowiedzialnych za spadek liczebności gatunku wymaga pilnych badań i adekwatnych działań ochronnych. (Zink et al. 2006). ...
This book is aimed to fulfil the gap in our knowledge on the distribution, numbers, habitat use and population trends of common breeding birds in Poland. We present here the detailed information on predicted spatial distributions for 80 bird species. For all of them, the habitat suitability maps are provided, prepared in the resolution of 1 × 1 km. The species distribution maps resulted from generalisation of rules and patterns revealed while modelling their habitat preferences, based on information gathered from more than 700 sampling plots spread across the country. For each species, beside maps showing spatial distribution of habitat suitability, we also include estimates of the total population, occupancy (in the 1 km grain), information on habitat preferences and population trends over the years 2000–2010. Additionally, based on the information on population trends and using IUCN regional criteria, we made assessments of the threat status for all species considered in the book. Finally, we showed regions within the country, which support largest populations of these common, although already threatened bird species. These hot-spots of declining common birds define areas where conservation actions should be targeted in the nearest future.
... Genetic results and comments on molecular markers.-Some authors have suggested that natural selection biases the pattern of variation in mtDNA genomes (Ballard and Whitlock 2004, Galtier et al. 2009:4546, Balloux 2010, but the question is whether selection is sufficiently strong to obscure evolutionary patterns and processes, which several studies suggest is not the case for birds (Zink 2005, Zink et al. 2006, Hung et al. 2012). Our HKA test revealed no evidence of strong selection that would bias mitochondrial or nuclear loci. ...
An important step in conservation is to identify whether threatened populations are evolutionarily discrete and significant to the species. A prior mitochondrial DNA (mtDNA) phylogeographic study of the California Gnatcatcher (Polioptila californica) revealed no geographic structure and, thus, did not support the subspecies validity of the threatened coastal California Gnatcatcher (P. c. californica). The U.S. Fish and Wildlife Service concluded that mtDNA data alone were insufficient to test subspecies taxonomy. We sequenced eight nuclear loci to search for historically discrete groupings that might have been missed by the mtDNA study (which we confirmed with new ND2 sequences). Phylogenetic analyses of the nuclear loci revealed no historically significant groupings and a low level of divergence (G(ST) = 0.013). Sequence data suggested an older population increase in southern populations, consistent with niche modeling that suggested a northward range expansion following the Last Glacial Maximum (LGM). The signal of population increase was most evident in the mtDNA data, revealing the importance of including loci with short coalescence times. The threatened subspecies inhabits the distinctive Coastal Sage Scrub ecosystem, which might indicate ecological differentiation, but a test of niche divergence was insignificant. The best available genetic, morphological, and ecological data indicate a southward population displacement during the LGM followed by northward range expansion, without the occurrence of significant isolating barriers having led to the existence of evolutionarily discrete subspecies or distinct population segments that would qualify as listable units under the Endangered Species Act. Received 19 December 2012, accepted 19 April 2013.
... EURASIAN TREECREEPER PHYLOGEOGRAPHY 11 several dispersal events between Corsica and the Caucasus region, two disjunct regions located about 2700 km from each other, seems highly unlikely knowing the poor over water dispersal abilities of the Eurasian treecreeper (Harrap, 2008) and the absence of corsa-caucasica haplotypes elsewhere in southern Europe. A third hypothesis would be that mtDNA did not evolve neutrally in the Eurasian treecreeper as it has been suggested for its relative the Eurasian nuthatch (Sitta europaea, Zink, Drovetski & Rohwer, 2006), the corsa-caucasica mitochondrial lineage being submitted to positive selection. Although we did not detect any evidence of selection with the MK tests, more data and statistical analyses would be necessary to dismiss the selection hypothesis (see Garvin et al., 2015 for a review). ...
In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub-species currently recognized, support the monophyly of C. familiaris with respect to its Indo-Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid-Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.9 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub-species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica.
... Finally, it has also been proposed to split S. carolinensis into four taxa (Walström et al. 2012). Although the taxonomic sampling could be denser at the tips of the nodes (for instance, in S. europaea; Zink et al. 2006;Hung et al. 2012), we confidently obtained a robust general phylogeny for the family that we used to investigate the ecological specialization of nuthatch lineages in breeding, as well as the foraging aspects of their life history. ...
A comprehensive phylogeny of the nuthatches, genus Sitta, is proposed based on 21 of the 24-28 species recognized in the genus and three genes, two mitochondrial (cytochrome b and cytochrome oxidase subunit I) and one nuclear (RAG1). This phylogeny is well resolved and reveals several major clades within nuthatches. Przevalski's Nuthatch Sitta przewalskii is sister to all other nuthatches, without any close relatives in our sampling. The larger species S. carolinensis and S. magna, despite their disjunct distributions, are sister taxa at the base of the tree. The next clade comprises the europaea group, which is sister to the two rock nuthatches (S. tephronota and S. neumayer), and to the Beautiful Nuthatch Sitta formosa of southeast Asia, although with less support. All these species use plastering to reduce the entrance of their hole or to build their nest with mud on rocks, but their ecologies are not as specialized as those of the rock nuthatches. The Asian small species (represented by S. azurea, S. frontalis and S. oenochlamys) form a well-supported clade. We confirm a single origin for the canadensis group that also includes the Yunnan nuthatch Sitta yunnanensis. Both are sister group to the two sibling species of North America (S. pygmaea and S. pusilla); all these species dig their own nest in trunks and are closely associated with coniferous forest. A biogeographical analysis supports the hypothesis of Asia being the center of diversification for nuthatches, with several independent dispersal events to North America.
... Most acadicus were from Alaska, but we also included individuals from New Mexico, Oregon, and Washington, USA, to encompass broader geographic variation (sample sizes varied by marker; see Figure 2 and Table 1). ND2 is a well-known marker in birds and has been shown to be particularly informative and approximately neutrally evolving (Zink et al. 2005); similarly, cyt b is a well-studied gene with a fairly constant rate of evolution (Moore andDeFilippis 1997, Avise 2000), allowing population parameters to be estimated with reasonable confidence (Lovette 2004). ...
Differentiation, often leading to speciation, is common among island populations of birds. However, migratory species tend to differentiate less because increased movements often preclude the extended periods of allopatry thought to be required for speciation. This interaction of isolation and migration-gene flow is a complex issue in evolutionary biology. We examined the genetics of divergence in Northern Saw-whet Owls (Aegolius acadicus), in which a migratory form (A. a. acadicus) occurs during fall migration and winter, but not at other times of the year, in the range of a sedentary, island form (A. a. brooksi) on HaidaGwaii, British Columbia. We used 2,018 base pairs of mtDNA and genomic data from 405 amplified fragment-length polymorphisms to assess the population genetics and evolutionary history of these two subspecies. Both mtDNA and nuclear genomic markers showed significant divergence between these subspecies, and mtDNA gene flow between them was very low (<1 individual generation-1). These subspecies likely diverged in association with the Wisconsin glacial maximum, similar to 16,000 yr BP. The refugial history of the region, life-history traits, and the maintenance of lineage integrity despite current contact suggest that this divergence occurred or is maintained through heteropatric differentiation, probably driven by a loss of migratory behavior in brooksi accompanied by local adaptations.
... Several studies have dealt with the phylogeography of widespread northern Palearctic animals, including mammals such as badger Meles meles [16], hares Lepus spp. [17], and various rodents [18][19][20][21][22][23], as well as birds including ducks [24], shorebirds [25,26], woodpeckers [27,28], and several species of passerines [26,[29][30][31][32][33][34][35][36][37][38][39][40][41]. ...
... Vaurie 1959, Harrap 1996. Zink et al. (2006) erwägen, diese drei Gruppen als Phylogenetische Arten (nach dem PSC) zu betrachten, unterbreiten indes keinen eindeutigen nomenklatorischen Vorschlag. Himalayanische, burmesische und chinesische Kleiber aus der S. europaea-Gruppe, die weitere markante Differenzierungen erwarten lassen, harren der genetischen und akustischen Analyse. ...
... To directly and quantitatively compare the sequence diversity contained within the two species, we calculated haplotype diversity (H D) and nucleotide diversity (n) for each species and locus. To address a key assumption behind inferring phylogeographical history from mitochondrial (mt)DNA sequences, namely, that sequences evolve in a selectively neutral fashion (Zink, Drovetski & Rohwer, 2006), we performed a series of neutrality tests, implemented in DNASP (Rozas et al., 2003). Tajima's D and Fu's F S were used to assess whether sequences had been subject to selection (Tajima, 1989;Fu, 1997) (e.g. a selective sweep). ...
Comparative phylogeography is underpinned by the assumption that sympatrically‐distributed taxa will have experienced similar environmental histories, resulting in broadly congruent spatial structuring of phylogenetic lineages, particularly if they inhabit similar niches. However, divergent local conditions, specifically those related to microhabitat, may produce significantly divergent systematic signatures of demographic histories. In the present study, we compare the phylogenetic and population genetic spatial patterns displayed by two species of niche‐separated (but sympatrically distributed) Australian funnel web spiders (Mygalomorphae: Hexathelidae). We demonstrate that an apparently minor disparity in habitat niche has led to divergent experiences of a common environmental history in the saproxylic Hadronyche cerberea and the ground‐burrowing Atrax sutherlandi. Furthermore, we take a crucial first step in documenting the molecular systematics of a group that has traditionally suffered from a dearth of research interest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 805–819.
... Relatively high levels of divergence were reported between Palearctic and Nearctic populations of some Holarctic birds (e.g. Drovetski et al. 2004;Koopman et al. 2005;Zink et al. 2006). The avifauna of the Japanese Archipelago includes many possible cryptic species, despite the differences in size and geographical history of the region. ...
DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 out of the 251 Japanese breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identigy Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding 6 duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology. This article is protected by copyright. All rights reserved.
... Vaurie 1959, Harrap 1996. Zink et al. (2006) erwägen, diese drei Gruppen als Phylogenetische Arten (nach dem PSC) zu betrachten, unterbreiten indes keinen eindeutigen nomenklatorischen Vorschlag. Himalayanische, burmesische und chinesische Kleiber aus der S. europaea-Gruppe, die weitere markante Differenzierungen erwarten lassen, harren der genetischen und akustischen Analyse. ...
... To certify that sequences were of mitochondrial origin, we checked for internal stop codons and calculated nucleotide diversity statistics. Following Zink et al. (2006), the McDonald– Kreitman test was used in DnaSP ver. 5.10 (Librado and Rozas 2009) to test for neutrality of ND2, and hence check that our phylogenetic inferences were not compromised by natural selection. ...
Knowledge of population structure and patterns of connectivity is required to implement effective conservation measures for the purple-crowned fairy-wren (Malurus coronatus), a threatened endemic of northern Australia. This study aimed to identify barriers to dispersal across the distribution of M. coronatus, investigate the impact that the recent declines may have on population connectivity, and propose conservation actions to maintain natural patterns of gene flow. Analysis of mitochondrial DNA sequences from 87 M. coronatus identified two phylogenetic clusters that corresponded with the phenotypically defined western (M. c. coronatus) and eastern (M. c. macgillivrayi) subspecies. The genetic divergence between these subspecies was consistent with isolation by a natural barrier to gene flow, and supports their separate conservation management. Within the declining M. c. coronatus, the lack of genetic divergence and only slight morphological difference between remnant populations indicates that populations were recently linked by gene flow. It is likely that widespread habitat degradation and the recent extirpation of M. c. coronatus from the Ord River will disrupt connectivity between, and dynamics within, remnant populations. To prevent further declines, conservation of M. coronatus must preserve areas of quality habitat and restore connectivity between isolated populations.
... McDonald-Kreitman tests were conducted using orthologous sequences from Gallus gallus and from a congeneric species, but revealed no significant deviations from selective neutrality (data not shown). These results are similar to those of Zink et al. (2006) on genetic variation in the ND2 gene in the Eurasian nuthatch (Sitta europaea). Across the 16 species we surveyed, there was broad congruence among the demographic statistics D, D*, and F*. ...
Islands offer unique opportunities for studies of evolution and historical demography. We hypothesized that wintering North American migrant bird species would show genetic evidence of population expansion over recent millennia due to the expansion of their breeding distributions following the retreat of the Laurentide ice sheet. In contrast, we presumed that non-migratory species would exhibit more stable historical demographies. We used mtDNA sequences from 649 individuals of 16 avian species on the Caribbean island of Hispaniola to test this prediction. Mismatch distributions did not differ significantly between migrants and non-migrants. However, neutrality indices indicated population expansion in the migrant species, as well as two non-migratory resident species with extensive distributions. Evidence of population expansion was less consistent in other non-migratory residents. We infer that climate prior to the Last Glacial Maximum significantly reduced effective population sizes of most migratory North American bird populations and some resident Hispaniolan bird populations. Our data further revealed that mismatch statistics were poorly correlated with and less informative than the neutrality test statistics, a consideration for future demographic studies.
... Perisoreus – Nucifraga – Baeolophus/ Lophophane Gill et al. (2005) Poecile Gill et al. (2005) Certhia Tietze et al. (2006) Sitta Zink et al. (2006a) Troglodytes T. troglodytes* Drovetski et al. (2004a) Regulus Päckert et al. (2003) Turdus Voelker et al. (2007) ...
Aim Boreal forest bird species appear to be divided into lineages endemic to each northern continent, in contrast to Holarctic species living in open habitats. For example, the three‐toed woodpecker ( Picoides tridactylus ) and the winter wren ( Troglodytes troglodytes ) have divergent Nearctic and Palaearctic mitochondrial DNA clades. Furthermore, in these species, the next closest relative of the Nearctic/Palaearctic sister lineages is the Nearctic clade, suggesting that the Palaearctic may have been colonized from the Nearctic. The aim of this study is to test this pattern of intercontinental divergence and colonization in another Holarctic boreal forest resident – the pine grosbeak ( Pinicola enucleator ).
Location The Holarctic.
Methods We sequenced the mitochondrial ND2 gene and Z ‐specific intron 9 of the ACO1 gene for 74 pine grosbeaks collected across the Holarctic. The sequences were used to reconstruct the phylogeographical history of this species using maximum likelihood analysis.
Results We discovered two distinct mitochondrial and Z ‐specific lineages in the Nearctic and one in the Palaearctic. The two Nearctic mtDNA lineages, one in the northern boreal forest and one in south‐western mountain forest, were more closely related to each other than either was to the Palaearctic clade. Two Nearctic Z‐chromosome clades were sympatric in the boreal and south‐western mountain forests. Unlike the topology of the mtDNA tree, the relationship among the Z‐chromosome clades was the same as in the three‐toed woodpecker and winter wren [Nearctic (Nearctic, Palaearctic)]. The Palaearctic Z‐chromosome clade had much lower genetic diversity and a single‐peak mismatch distribution with a mean < 25% of that for either Nearctic region, both of which had ragged mismatch distributions.
Main conclusions Our data suggest that, similar to the other boreal forest species, the pine grosbeak has divergent lineages in each northern continent and could have colonized the Palaearctic from the Nearctic. Compared with many Holarctic birds inhabiting open habitats, boreal forest species appear to be more differentiated, possibly because the boreal forests of the Nearctic and Palaearctic have been isolated since the Pliocene (3.5 Ma).
... It is possible that in avoiding CR, researchers have abandoned a valuable source of information about evolutionary patterns and processes. Here, we investigate these questions by comparing genealogical and population genetic inferences obtained using samples from the CR and mitochondrial NADH dehydrogenase subunit 2 (ND2, a protein-coding gene commonly used in avian population-level studies;293031) gene of the red-winged blackbird (Agelaius phoeniceus). Inference of population processes from molecular data is assumption-laden, and it has become increasingly clear that the complexity of evolutionary dynamics in mitochondrial DNA, and in particular of the CR, has significant implications for such inference. ...
Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (Agelaius phoeniceus) and its close relative the tricolored blackbird (A. tricolor). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for A. phoeniceus. However, individual Sanger-read-length fragments (∼600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.
... Additionally, in forest bird species, the Caucasus appears to be an area of genetic divergence. Endemic (or nearly so) clusters of haplotypes in the Caucasus have been documented for several species (Carpodacus erythrinus, Motacilla alba, Sitta europaea, Troglodytes troglodytes; reviewed by Zink et al. [83]). ...
Some decades ago, biogeographers distinguished three major faunal types of high importance for Europe: (i) Mediterranean elements with exclusive glacial survival in the Mediterranean refugia, (ii) Siberian elements with glacial refugia in the eastern Palearctic and only postglacial expansion to Europe and (iii) arctic and/or alpine elements with large zonal distributions in the periglacial areas and postglacial retreat to the North and/or into the high mountain systems. Genetic analyses have unravelled numerous additional refugia both of continental and Mediterranean species, thus strongly modifying the biogeographical view of Europe. This modified notion is particularly true for the so-called Siberian species, which in many cases have not immigrated into Europe during the postglacial period, but most likely have survived the last, or even several glacial phases, in extra-Mediterranean refugia in some climatically favourable but geographically limited areas of southern Central and Eastern Europe. Recently, genetic analyses revealed that typical Mediterranean species have also survived the Last Glacial Maximum in cryptic northern refugia (e.g. in the Carpathians or even north of the Alps) in addition to their Mediterranean refuge areas.
A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
In the first half of the 20th century the German ornithologist Hugo Weigold was one of the pioneers in the emerging field of biogeography. As a member of Walther Stötzner’s expedition to Sichuan and Tibet (1913-1915) he was among the first Western researchers to study the immense species richness of the Chinese avifauna. Today, his rich collections of bird skins from China are housed in nearly equal parts at the Natural History Museums of Berlin and Dresden and from this material many taxa were described as new to science. Several of these are accepted as good species today and some are even representatives
of the endemic avifauna of China. In his early work already Weigold hypothesized a Tibetan center of origin and diversification from where ancestors of extant species dispersed northwards and colonized the Northern and Western Palaearctic. This idea received recent support from genetic studies that found evidence of a Tibetan cradle of evolution for example in alpine plants and cold-adapted mammals. Furthermore, modern analytical methods allow for genetic analysis of the 100-year-old specimens collected by Weigold and his contemporaries. In this respect, type specimens are of utmost mportance for the authoritative assignment of taxon names to genetic lineages. When it was finally published after his death, Weigold’s monograph on the biogeography of Tibet and its forelands still featured some visionary thoughts on the evolutionary history of faunal assemblages of the Tibetan Plateau and the mountain ranges at its margins. Today, some of Weigold’s original ideas have received support from modern phylogenetic and phylogeographic studies, including examples from our own research group.
The common stonechat Saxicola torquatus traditionally was considered as a polytypic species widely distributed in Africa, Europe and
Asia. Recently, several authors have suggested that this formerly single species needs to be split into several distinct species composing
the Saxicola torquatus complex based on mitochondrial markers. However, mitochondrial DNA alone is not sufficient for the evaluation
of species status. In this paper, we reviewed the taxonomy of Northern Eurasian taxa from the complex based on morphometrics, plumage,
song and alarm calls. The morphological and vocal data clearly matched the phylogroups reconstructed from mitochondrial DNA
sequences, and separated Northern Eurasian taxa of the Saxicola torquatus complex into three groups: rubicola, maurus and stejnegeri. We
proposed the species status for these three groups: European stonechat Saxicola rubicola, eastern stonechat Saxicola maurus and Japanese
stonechat Saxicola stejnegeri. Among them, S. stejnegeri is a cryptic species as it cannot be distinguished by morphometrics and by worn
spring plumage from S. maurus, but differs noticeably by male song.
The scientific names and taxonomy adopted by the Check-List of Japanese Birds 7th edition published in 2012 was reviewed for 154 taxa belonging to15 families in the order Passeriformes, focusing on discrepancies from the 6th edition and the IOC World Bird List, mainly in light of the latest molecular phylogeny. Fifty taxa differed from the 6th edition and twenty-five taxa differed from the IOC list. Whereas the majority of the taxa in the 7th edition reflected the latest molecular phylogeny, some taxa in the Fringillidae and Corvidae did not. In the Fringillidae, Carduelis spinus should be moved to the genus Spinus, and C. flammea and C. hornemanni should be moved to the genus Acanthis. The range of Corvus corone is questionable, and the taxonomy of Pica pica and related taxa should be reconsidered. Molecular phylogenetic studies, published since the 7th edition, have advocated different names for Paridae and Fringillidae than those adopted by the 7th edition. It is advocated that Poecile varius should be moved to the genus Sittiparus and that two subspecies are elevated to full species. Both Uragus sibiricus and Chaunoproctus ferreorostris are to be moved to the genus Carpodacus. Passer rutilans should be renamed Passer cinnamomeus based on the Principle of Priority, although that is not a taxonomic subject. We were unable to give the correct spelling for Artamus leucorynchus because of a loophole in the International Code of Zoological Nomenclature. In past editions of the check list of Japanese birds, many taxa have been considered to be junior synonyms and removed from the list, without sufficient scientific evidence. Therefore, the check list of Japanese birds may be revised on a large scale in the future.
Reverse colonization from an island to a continent runs counter to the classic models of speciation in island biogeography. We mined the Barcode of Life Data Systems and generated mitochondrial DNA-based phylogenetic analyses for 118 Japanese bird species to identify candidates for reverse colonization histories from Japan to mainland Asia. Mitochondrial DNA tree topologies suggested 5 strong and 35 weak candidate species for reverse colonization from Japan to mainland Asia. Thirty-nine mitochondrial DNA topologies contradicted a reverse colonization hypothesis. For the remaining 39 species the ancestral distribution is ambiguous from the available mitochondrial DNA gene tree topology. A combination of geography and climatic and geologic history are likely drivers of avian speciation in the Japanese Islands and subsequent reverse colonization events to mainland Asia. These data highlight the utility of large scale DNA barcoding databases in generating phylogenetic and biogeographic hypotheses.
We studied the phylogeography and population history of the White Wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of White Wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in Central and South Europe; and clade SE was distributed in Central and East Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of East Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.
The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescent-based simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without
phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions
and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic
regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based
on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher
in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides
valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions
of the world.
The green woodpecker complex consists of the green woodpecker (Picus viridis), distributed from Western Europe to the Caucasus and Iran, and the related LeVaillant's woodpecker (P. vaillantii), distributed in north‐western Africa from central Morocco to Tunisia. Much of the habitat of green woodpeckers in Central and Northern Europe was covered by ice, tundra, steppe or other unsuitable habitat during the Pleistocene; consequently, they must have come to occupy most of their current range during the past 20 000 years. We used complete mitochondrial ND2 sequences from populations throughout the range to investigate the genetic structure and evolutionary history of this complex. Three well‐differentiated clades, corresponding to three biogeographical regions, were recovered; 89% of the total genetic variance was distributed among these three regions. The populations in North Africa were sister to those of Europe and, within Europe, Iberia was sister to the rest of Europe and the Near East. This suggests that the post‐glacial colonization of most of Europe occurred from a refuge east of Iberia, probably in Italy or the Balkans; there was no substantial divergence among these regions. In addition, a population sample from Iran was genetically distinct from those of Western Europe, indicating a history of genetic isolation and an additional Pleistocene refuge east of the well‐known Balkan refugia and south of the Caucasus. Within Europe, northern populations were less genetically variable than southern ones, consistent with recent colonization. There was significant isolation‐by‐distance across Europe, indicating restricted gene flow; this was particularly apparent between western populations and those of the Caucasus and Iran. We recognize four species in the complex. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 710–723.
We analyzed sequences of two mitochondrial DNA gene regions (control region and ND2) from 186 specimens obtained from 17 Eurasian localities covering most of the distribution of the common roseWnch to assess phylogeographic structure. Populations pos- sessed a high level of nucleotide diversity relative to many other Palearctic species, suggesting that roseWnch populations are rela- tively old and possess high eVective sizes. Mismatch distributions suggested that many localities experienced past population expansions, which are older than those expected for post-Pleistocene climate warming and reforestation of Eurasia. Our st analysis revealed that 12.4% of total genetic variation was distributed among localities owing in part to the existence of three incompletely isolated groups: southwestern (subspecies C. e. kubanensis), northeastern (subspecies C. e. grebnitskii), and northwestern (subspecies C. e. erythrinus and C. e. ferghanensis). The three groups are not reciprocally monophyletic which suggests that they were formed rel- atively recently. Gene Xow among groups is restricted. Coalescence analysis indicated dispersal asymmetry.
We conducted phylogeographic analyses of Motacilla flava (Yellow Wagtail) and M. citreola (Citrine Wagtail). We analyzed mitochondrial DNA sequences from 167 M. flava specimens obtained from 17 localities throughout Eurasia and Alaska, and 38 specimens of M. citreola obtained from 7 Eurasian localities. Phylogenetic analysis revealed three clades within traditionally recognized M. flava: Europe and southwestern Asia, northeastern Eurasia, and southeastern Asia. Those groups should be considered species, because together they are not monophyletic, and are interspersed with M. citreola, M. cinerea, and M. alba. Motacilla citreola also is paraphyletic, consisting of two species-level groups. Northeastern and southeastern groups of M. flava each appear to be sister taxa to eastern and western groups of M. citreola, respectively. Together those four groups form a clade, whereas the western M. flava group is considerably more distant. Within each of the three groups of M. flava, and the two groups of M. citreola, little phylogeographic structure was detected. Signatures of past population expansion are evident for some populations of M. flava; expansion is more recent in Moscow, Kursk (western group), Yamal, and Anabar (northeastern group), and older in Tyva and Vyatka (western group). A history of population stability is inferred for the Yamal population of M. citreola. Nested-clade analyses detected contiguous range expansion for southeastern M. flava and restricted gene flow with isolation by distance for northeastern M. flava and eastern M. citreola.
We compared mitochondrial DNA sequences of Three-toed Woodpeckers (Picoides tridactylus) within and between Eurasia and North America. Samples from the two continents are each reciprocally monophyletic, and differ by approximately 4% sequence divergence, suggesting that a separate species exists on each continent. We recommend formal taxonomic action. Within continents, no phylogeographic structuring was found, suggesting that both species have recently expanded their ranges following the end of the last ice age. Filogeografía Holártica y Límites de la Especie Picoides tridactylus Resumen. Comparamos secuencias de ADN mitocondrial en Picoides tridactylus, dentro y entre Eurasia y América del Norte. Las muestras de cada uno de los dos continentes son recíprocamente monofiléticas y difieren aproximadamente en un 4% de divergencia secuencial, sugiriendo que existe una especie distinta en cada continente. Recomendamos acción taxonómica formal. No encontramos estructura filogeográfica dentro de los continentes, sugiriendo que ambas especies han expandido recientemente sus rangos luego del final de la última era glacial.
We analyzed sequences of two mitochondrial DNA (mtDNA) gene regions (control region and ND2) totaling 1477 base-pairs from 232 specimens of the white wagtail Motacilla alba obtained from 27 localities throughout Eurasia. Although overall haplotype diversity was relatively low (0.79) and the most common haplotype was shared by 45% of individuals, belonging to six subspecies, a high level of population differentiation was detected. The mtDNA tree revealed three clades: (1) most individuals from Krasnodar (belonging to M. a. alba subspecies), (2) all individuals from Almaty and some from Primor'e (belonging to M. a. personata, M. a. lugens and M. a. leucopsis subspecies), and (3) the remaining individuals (representing all subspecies and all localities except Almaty). We suggest that these three clades represent historically isolated populations that relatively recently came into secondary contact in Krasnodar and Primor'e. None of the six subspecies were reciprocally monophyletic in the mtDNA tree. The Krasnodar population appeared to receive immigrants from other localities, but distinctive haplotypes from this locality did not appear elsewhere, suggesting asymmetric gene flow. Signatures of recent gene flow between northern populations were detected, and there was no evidence of isolation by distance within the northern group of populations. Mismatch distributions for most localities were consistent with population expansions. We also analyzed 12 male plumage characters from 93 study skins sampled from 24 populations. Phylogenetic trees resulting from separate genetic and morphological analyses were incongruent. Plumage evolution seems to be under strong sexual or natural selection, which favors particular phenotypes in various areas irrespective of the mitochondrial background. Dispersal events at different evolutionary times could have obscured the effects of earlier isolation events. The mtDNA data does not support species status for M. a. lugens and M. a. personata, which shared haplotypes with other subspecies of M. alba. We recommend that M. lugens and M. personata are placed as junior synonyms of M. alba.
We sequenced parts of three mitochondrial genes in 67 great spotted woodpeckers Dendrocopos major taken from 17 sites across Eurasia and Japan. Two groups, differing by ca. 3% sequence divergence, were determined to have had independent evolutionary histories: samples from the southeast (Sakhalin, Primor'e, Hokkaido), and the rest of Eurasia. The southeastern group corresponds to the subspecies D. m. japonicus, which will likely merit species status upon study of all subspecies; at present it should be considered an evolutionarily significant unit. From the United Kingdom to the Russian North Pacific, no phylogeographic divisions were found, which is likely a result of recent range expansion following retreat of permafrost after the last ice age.
We used maximum likelihood analysis of complete mitochondrial ND2 sequences (1041 bp) to clarify the taxonomy and relationships of various species and genera of grass and bush warblers. The tree revealed two clades of grass and bush warblers. One clade was comprised of all four western Palearctic Locustella and two species of Asian Bradypterus. The other clade included five eastern Palearctic Locustella (including the distinctive Sakhalin warbler Locustella amnicola) and the marsh grassbird Megalurus pryeri. African Bradypterus and Australian little grassbird Megalurus gramineus were distantly related to their Asian congeners. Therefore, current taxonomy of these genera does not reflect their evolutionary history and needs revision. It is proposed that a phylogenetic analysis of morphology and ecological preferences would show that the current taxonomy of grass and bush warblers reflects species’ habitat preferences and morphology related to locomotion and foraging in their habitats, rather than their shared ancestry. Distinct clades were found in grasshopper warbler Locustella naevia and Pallas's grasshopper warbler L. certhiola. Detailed phylogeographic studies are needed to elucidate the species status of the clades within these two species.
Unlabelled:
We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.
Availability:
http://www.megasoftware.net.
Contact:
s.kumar@asu.edu
DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and
features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number
of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene
flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical
outputs for an easy visualization of results.
Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.
We introduce the genealogy of a random sample of genes taken from a large haploid population that evolves according to random reproduction with selection and mutation. Without selection, the genealogy is described by Kingman's well-known coalescent process. In the selective case, the genealogy of the sample is embedded in a graph with a coalescing and branching structure. We describe this graph, called the ancestral selection graph, and point out differences and similarities with Kingman's coalescent. We present simulations for a two-allele model with symmetric mutation in which one of the alleles has a selective advantage over the other. We find that when the allele frequencies in the population are already in equilibrium, then the genealogy does not differ much from the neutral case. This is supported by rigorous results. Furthermore, we describe the ancestral selection graph for other selective models with finitely many selection classes, such as the K-allele models, infinitely-many-alleles models. DNA sequence models, and infinitely-many-sites models, and briefly discuss the diploid case.
Patterns of gene differences among humans contain information about the demographic history of our species. Haploid loci like mitochondrial DNA and the nonrecombining part of the Y chromosome show a pattern indicating expansion from a population of only several thousand during the late middle or early upper Pleistocene. Nuclear short tandem repeat loci also show evidence of this expansion. Both mitochondrial DNA and the Y chromosome coalesce within the last several hundred thousand years, and they cannot provide information about the population before their coalescence. Several nuclear loci are informative about our ancestral population size during nearly the whole Pleistocene. They indicate a small effective size, on the order of 10,000 breeding individuals, throughout this time period. This genetic evidence denies any version of the multiregional model of modern human origins. It implies instead that our ancestors were effectively a separate species for most of the Pleistocene.
An excess of nonsynonymous substitutions over synonymous ones is an important indicator of positive selection at the molecular level. A lineage that underwent Darwinian selection may have a nonsynonymous/synonymous rate ratio (dN/dS) that is different from those of other lineages or greater than one. In this paper, several codon-based likelihood models that allow for variable dN/dS ratios among lineages were developed. They were then used to construct likelihood ratio tests to examine whether the dN/dS ratio is variable among evolutionary lineages, whether the ratio for a few lineages of interest is different from the background ratio for other lineages in the phylogeny, and whether the dN/dS ratio for the lineages of interest is greater than one. The tests were applied to the lysozyme genes of 24 primate species. The dN/dS ratios were found to differ significantly among lineages, indicating that the evolution of primate lysozymes is episodic, which is incompatible with the neutral theory. Maximum-likelihood estimates of parameters suggested that about nine nonsynonymous and zero synonymous nucleotide substitutions occurred in the lineage leading to hominoids, and the dN/dS ratio for that lineage is significantly greater than one. The corresponding estimates for the lineage ancestral to colobine monkeys were nine and one, and the dN/dS ratio for the lineage is not significantly greater than one, although it is significantly higher than the background ratio. The likelihood analysis thus confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages.
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Distributions of pairwise differences often called "mismatch distributions" have been extensively used to estimate the demographic parameters of past population expansions. However, these estimations relied on the assumption that all mutations occurring in the ancestry of a pair of genes lead to observable differences (the infinite-sites model). This mutation model may not be very realistic, especially in the case of the control region of mitochondrial DNA, where this methodology has been mostly applied. In this article, we show how to infer past demographic parameters by explicitly taking into account a finite-sites model with heterogeneity of mutation rates. We also propose an alternative way to derive confidence intervals around the estimated parameters, based on a bootstrap approach. By checking the validity of these confidence intervals by simulations, we find that only those associated with the timing of the expansion are approximately correctly estimated, while those around the population sizes are overly large. We also propose a test of the validity of the estimated demographic expansion scenario, whose proper behavior is verified by simulation. We illustrate our method with human mitochondrial DNA, where estimates of expansion times are found to be 10-20% larger when taking into account heterogeneity of mutation rates than under the infinite-sites model.
The evolutionary divergence of a single species into two has never been directly observed in nature, primarily because speciation can take a long time to occur. A ring species, in which a chain of intergrading populations encircles a barrier and the terminal forms coexist without interbreeding, provides a situation in which variation in space can be used to infer variation in time. Here we reconstruct the pathway to speciation between two reproductively isolated forms of greenish warbler (Phylloscopus trochiloides). These two taxa do not interbreed in central Siberia but are connected by a long chain of intergrading populations encircling the Tibetan Plateau to the south. Molecular data and climatic history imply that the reproductively isolated taxa came into contact following expansions northward around the western and eastern sides of the plateau. Parallel selection pressures for increased song complexity during the northward expansions have been accompanied by divergence in song structure. Playback experiments show that the two Siberian forms do not recognize each other's songs. Our results show how gradual divergence in a trait involved in mate choice leads to the formation of new species.
We examine variation among species of Mus in four genes involved in reproduction and the immune response for evidence of positive selection: the sperm recognition gene Zp-3, the testis-determining locus Sry, the testicular cell surface matrix protein Tcp-1, and the immune system protein β2m. We use likelihood ratio tests in the context of a well-supported phylogeny to determine whether models that allow for positively selected sites fit the sequences better than models that assume purifying selection. We then apply a Bayesian approach to identify particular sites in each gene that have a high posterior probability of being under positive selection. We find no evidence of positive selection on the Tcp-1 gene, but for Zp-3, Sry, and β2m, models that allow for positively selected sites fit the sequences better than alternatives. For each of these genes, we identify sites that have a high (> 95%) posterior probability of being positively selected. For Zp-3, two of these sites occur near the sperm-binding region, while one occurs in a region whose functional role remains unstudied but where the pattern of change predicts functional importance. A single site in Sry shows an elevated rate of replacement substitution but occurs in a region of apparently little functional importance; therefore, relaxation of functional constraints may better explain the rapid evolution of this site. Three sites in β
2m have a posterior probability > 50% of being under positive selection. While the functional role for two of these sites is unknown, the third is known to influence the ability of MHC class I molecules to present antigens to the immune system; therefore, the elevated rate of replacement substitutions at this site is consistent with selection acting to promote variability in immune system proteins.
The great tit complex is divided into four groups, each containing several subspecies. Even though the groups are known to differ markedly on morphological, vocal and behavioural characters, some hybridization occurs in the regions where they meet. The great tit has often been referred to as an example of a ring species, although this has later been questioned. Here, we have studied the genetic structure and phylogenetic relationships of the subspecies groups to clarify the evolutionary history of the complex using control region sequences of the mitochondrial DNA. The subspecies groups were found to be monophyletic and clearly distinct in mitochondrial haplotypes, and therefore must have had long-independent evolutionary histories. This conflicts with the ring species assignment and supports the formation of secondary contact zones of previously temporarily isolated groups. According to the phylogenetic species concept, all the subspecies groups could be considered as separate species, but if the definition of the biological species concept is followed, none of the subspecies groups is a true species because hybridization still occurs.
DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. AVAILABILITY: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
Our analysis of the ND2 sequences revealed six clades within winter wrens (Troglodytes troglodytes). These clades corresponded to six geographical regions: western Nearctic, eastern Nearctic, eastern Asia, Nepal, Caucasus and Europe, and differed by 3-8.8% of sequence divergence. Differences among regions explained 96% of the sequence variation in winter wren. Differences among individuals within localities explained 3% of the sequence variation, and differences among localities within regions explained 1%. Grouping sequences into subspecies instead of localities did not change these proportions. Proliferation of the six clades coincided with Early and Middle Pleistocene glaciations. The distribution of winter wren clades can be explained by a series of five consecutive vicariant events. Western Nearctic wrens diverged from the Holarctic ancestor 1.6 Myr before the present time (MYBP). Eastern Nearctic and Palaearctic wrens diverged 1 MYBP. Eastern and western Palaearctic birds diverged 0.83 MYBP. Nepalese and east Asian wrens diverged 0.67 MYBP, and Caucasian birds diverged from European wrens 0.54 MYBP. The winter wren has a much greater degree of inter- and intracontinental differentiation than the three other Holarctic birds studied to date--dunlin (Calidris alpina), common raven (Corvus corax) and three-toed woodpecker (Picoides trydactylus)--and represents an example of cryptic speciation that has been overlooked.
McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Genetic variability within and among 10 geographically distinct populations of Greenfinches (Carduelis chloris) was assayed by directly sequencing a 637 BP part of the mtDNA control region from 194 individuals. Thirteen variable positions defined 18 haplotypes with a maximum sequence divergence of 0.8% Haplotype (h = 0.28-0.77) and nucleotide (pi = 0.058-0.17%) diversities within populations were low, and decreased with increasing latitude (h:r(s) = -0.81; pi: r(s) = -0.89). The distribution of pairwise nucleotide differences fit better with expectations of a ''sudden expansion'' than of an ''equilibrium'' model, and the estimates of long term effective population sizes were considerably lower than current census estimates, especially in northern European samples. Selection is an unlikely cause of observed patterns because the distribution of variability conformed to expectations of neutral infinite alleles model and haplotype diversity across populations was positively correlated with heterozygosity !HE) in nuclear genes (I; = 0.74, P < 0.05). Hence, a recent bottleneck, followed by serial bottlenecking during the process of post-Pleistocene recolonization of northern Europe, together with recent population expansion provide a plausible explanation for the low genetic diversity in the north. Genetic distances among populations showed a clear pattern of isolation-by-distance, and 14% of the haplotypic variation was among populations, the rest being distributed among individuals within populations. In accordance with allozyme and morphological data, a hierarchical analysis of nucleotide diversity recognized southern European populations as distinct from northern European ones. However, the magnitude of divergence in mtDNA, allozymes and morphology were highly dissimilar (morphology > mtDNA > allozymes).
The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
A method for prediction of transmembrane segments from multiply aligned amino acid sequences is presented. For the calculations, two sets of propensity values were used: one for the middle, hydrophobic portion and one for the terminal regions of the transmembrane sequence spans. Average propensity values were calculated for each position along the alignment, with the contribution from each sequence weighted according to its dissimilarity relative to the other aligned sequences. Eight-residue segments were considered as potential cores of transmembrane segments and elongated if their middle propensity values were above a given threshold. End propensity values were also considered as stop signals. Only helices with length of 15 to 29 residues were allowed and corrections for strictly conserved charged residues were also made. The method is shown to be more successful than predictions based upon single sequences alone. In the test set of 28 families with 126 transmembrane segments, only five spans were not predicted or constituted false positives. The method is applied to sequence families for which data on transmembrane segments do not exist or are sparse or contradictory included voltage-gated potassium-channels, cytochrome c oxidases, NADH-ubiquinone oxidoreductase, beta-glucosides-specific phosphotransferase enzyme and major surface antigen of hepatitis B virus.
The main purpose of this article is to present several new statistical tests of neutrality of mutations against a class of alternative models, under which DNA polymorphisms tend to exhibit excesses of rare alleles or young mutations. Another purpose is to study the powers of existing and newly developed tests and to examine the detailed pattern of polymorphisms under population growth, genetic hitchhiking and background selection. It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations. Background selection gives rise to quite different polymorphic patterns than does logistic population growth or genetic hitchhiking, although all of them show excesses of rare alleles or young mutations. We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed.
To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as TAJIMA's D test, and the D and F tests proposed by FU and LI, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a "neutral" marker in evolutionary and population genetic studies.
Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.
McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.
Distribution of mitochondrial DNA cytochrome b gene haplotypes in two crow species was examined by means of sequencing of the 336-bp gene fragment. The topology of the NJ and UPGMA trees showed that the carrion crow range was split into two parts due to the presence of significantly diverged ancestral lineage localized in the southeastern part of the range. The carrion crow populations, inhabiting a territory ranging from France to northern Sakhalin, along with interspersed hooded crow populations and hybrid Siberian populations, shared a common haplotype. The border between two carrion crow lineages revealed is located in central Sakhalin. The subdivision of two weakly differentiated lineages within the jungle crown range, also observed within this territory, coincided with the subspecies division of this species. The estimated genetic distances indicate the isolation of the subgenus Coloeus. These data also suggest the convergent similarity between the chough Pyrrhocorax pyrrhocorax and the Corvus genus, as well as the conspecificity of Corvus corone corone and C. c. cornix.
Positive selection or adaptive evolution is thought to be responsible, at least some of the time, for the rapid accumulation of advantageous changes in protein-coding genes. The origin of new enzymatic functions, erection of barriers to heterospecific fertilization, and evasion of host response by pathogens, among other things, are thought to be instances of adaptive evolution. Detecting positive selection in protein-coding genes is fraught with difficulties. Saturation for sequence change, codon usage bias, ephemeral selection events and differential selective pressures on amino acids all contribute to the problem. A number of solutions have been proposed with varying degrees of success, however they suffer from limitations of not being accurate enough or being prohibitively computationally intensive. We have developed a character-based method of identifying lineages that undergo positive selection. In our method we assess the possibility that for each internal branch of a phylogenetic tree an event occurred that subsequently gave rise to a greater number of replacement substitutions than might be expected. We classify these replacement substitutions into two categories - whether they subsequently became invariable or changed again in at least one descendent lineage. The former situation indicates that the new character state is under strong selection to preserve its new identity (directional selection), while the latter situation indicates that there is a persistent pressure to change identity (non-directional selection). The method is fast and accurate, easy to implement, sensitive to short-lived selection events and robust with respect to sampling density and proportion of sites under the influence of positive selection.
We analysed mitochondrial DNA (mtDNA) sequences from 154 bluethroats (Luscinia svecica) sampled at 21 sites throughout much of their Eurasian range. A previously reported, single base-pair mtDNA difference between L. s. svecica and L. s. namnetum was inconsistent upon expanded geographical sampling. A significant FST value (0.29) and an isolation-by-distance effect show the existence of geographical differentiation. Phylogenetic analysis of haplotypes revealed northern and southern groups, although lineage sorting is incomplete. There was no geographical structure to the haplotype tree within groups, and currently recognized subspecies were not supported. A minimum evolution tree based on pairwise mtDNA genetic distances among average samples showed the same two broadly distributed northern and southern groups. These groups abut in the centre of the latitudinal range, and were possibly isolated by forest that developed and spread westward over the last 15 000 years. Pairwise FST values averaged 0.16 in the southern group, 0.04 in the northern group, and 0.42 between groups. Mismatch distributions suggested population growth in each group, with that in the south being more recent. In the northern group, the geographical pattern in tau suggested northward and eastward expansion. Analysis of nucleotide diversity suggested westward expansion in the southern group. The northern group had higher nucleotide diversity than the southern group, consistent with a larger current population size in the north. Given the significant FST, incompletely sorted haplotype tree, and broadly patterned minimum evolution tree, L. svevica appears to represent a species at an intermediate stage of differentiation between panmixia and reciprocal monophyly.
Subspecies are often used in ways that require their evolutionary independence, for example as proxies for units of conservation. Mitochondrial DNA sequence data reveal that 97% of continentally distributed avian subspecies lack the population genetic structure indicative of a distinct evolutionary unit. Subspecies considered threatened or endangered, some of which have been targets of expensive restoration efforts, also generally lack genetic distinctiveness. Although sequence data show that species include 1.9 historically significant units on average, these units are not reflected by current subspecies nomenclature. Yet, it is these unnamed units and not named subspecies that should play a major role in guiding conservation efforts and in identifying biological diversity. Thus, a massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.
Mitochondrial DNA (mtDNA) has been used to study molecular ecology and phylogeography for 25 years. Much important information has been gained in this way, but it is time to reflect on the biology of the mitochondrion itself and consider opportunities for evolutionary studies of the organelle itself and its ecology, biochemistry and physiology. This review has four sections. First, we review aspects of the natural history of mitochondria and their DNA to show that it is a unique molecule with specific characteristics that differ from nuclear DNA. We do not attempt to cover the plethora of differences between mitochondrial and nuclear DNA; rather we spotlight differences that can cause significant bias when inferring demographic properties of populations and/or the evolutionary history of species. We focus on recombination, effective population size and mutation rate. Second, we explore some of the difficulties in interpreting phylogeographical data from mtDNA data alone and suggest a broader use of multiple nuclear markers. We argue that mtDNA is not a sufficient marker for phylogeographical studies if the focus of the investigation is the species and not the organelle. We focus on the potential bias caused by introgression. Third, we show that it is not safe to assume a priori that mtDNA evolves as a strictly neutral marker because both direct and indirect selection influence mitochondria. We outline some of the statistical tests of neutrality that can, and should, be applied to mtDNA sequence data prior to making any global statements concerning the history of the organism. We conclude with a critical examination of the neglected biology of mitochondria and point out several surprising gaps in the state of our knowledge about this important organelle. Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance.
I examined mitochondrial ND2 sequences in species of tits (genus Parus) to determine whether substitutions were neutral or under selection. Haplotype trees in these species are shallow and geographically unstructured, which could be a signature of recent demographic expansion or purifying selection. McDonald-Kreitman tests revealed a pattern of excess replacement polymorphisms for closely related taxa. Replacement substitutions tended to be less common in the basal parts of haplotype trees, suggesting that they are selected against over evolutionary time. Thus, the pattern of selection is consistent with a model of mildly deleterious haplotypes. To investigate the significance of this selection, the ND2 gene was subdivided into surface and transmembrane portions, and synonymous-non-synonymous sites, and F(ST)-values (the amount of variance distributed among populations) computed for each. Among sampling localities in P. major, both partitions gave similar estimates of F(ST), which is consistent with demographic expansion as the cause of the shallow trees. In P. montanus, two localities contained high percentages of individuals that had a single replacement substitution in the transmembrane portion of the gene, which inflated F(ST)-values relative to the surface sites. Thus, the interpretation of the genetic differentiation of these two sites could be either geographical isolation or selection. Given that the sole substitution causing the high F(ST)-values was a replacement one, selection is implicated. However, this substitution occurred in only 2 of 12 localities, revealing that overall the phylogeographic pattern was not biased by selection, once the cause of the two high pairwise F(ST)-comparisons was recognized. Investigators should consider the source of significant genetic heterogeneity within species, to determine if the variation is likely caused by demographic isolation or selection. However, it seems unlikely that most phylogeographic analyses are invalidated by the effects of natural selection.
We analyzed sequences of two mitochondrial DNA gene regions (control region and ND2) from 186 specimens obtained from 17 Eurasian localities covering most of the distribution of the common rosefinch to assess phylogeographic structure. Populations possessed a high level of nucleotide diversity relative to many other Palearctic species, suggesting that rosefinch populations are relatively old and possess high effective sizes. Mismatch distributions suggested that many localities experienced past population expansions, which are older than those expected for post-Pleistocene climate warming and reforestation of Eurasia. Our Phi(st) analysis revealed that 12.4% of total genetic variation was distributed among localities owing in part to the existence of three incompletely isolated groups: southwestern (subspecies C. e. kubanensis), northeastern (subspecies C. e. grebnitskii), and northwestern (subspecies C. e. erythrinus and C. e. ferghanensis). The three groups are not reciprocally monophyletic which suggests that they were formed relatively recently. Gene flow among groups is restricted. Coalescence analysis indicated dispersal asymmetry.
The coalescent process can describe the effects of selection at linked loci only if selection is so strong that genotype frequencies evolve deterministically. Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects of weak selection. We show that the overall effect is given by an extension to Price's equation: the change in properties such as moments of coalescence times is equal to the covariance between those properties and the fitness of the sample of genes. The distribution of coalescence times differs substantially between allelic classes, even in the absence of selection. However, the average coalescence time between randomly chosen genes is insensitive to the current allele frequency and is affected significantly by purifying selection only if deleterious mutations are common and selection is strong (i.e., the product of population size and selection coefficient, Ns>3). Balancing selection increases mean coalescence times, but the effect becomes large only when mutation rates between allelic classes are low and when selection is extremely strong. Our analysis supports previous simulations that show that selection has surprisingly little effect on genealogies. Moreover, small fluctuations in allele frequency due to random drift can greatly reduce any such effects. This will make it difficult to detect the action of selection from neutral variation alone.
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