Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analysed patterns of hybridization and phenotypic variation across two newly discovered hybrid zones between three subspecies of barn swallow (Hirundo rustica). These subspecies differ in ventral coloration and wing length, traits that are targets of sexual and natural selection, respectively, and are associated with genome‐wide differentiation in allopatry. We tested the hypothesis that the degree of divergence in these traits is associated with the extent of hybridization in secondary contact. We applied measures of population structure based on >23,000 SNPs to confirm that named subspecies correspond to distinct genomic clusters, and assessed coincidence between geographic clines for ancestry and phenotype. Although gene flow was ongoing across both hybrid zones and pairwise F_ST between subspecies was extremely low, we found striking differences in the extent of hybridization. In the more phenotypically differentiated subspecies pair, clines for ancestry, wing length and ventral coloration were steep and coincident, suggestive of strong isolation and, potentially, selection associated with phenotype. In the less phenotypically differentiated pair, gene flow and phenotypic variation occurred over a wide geographic span, indicative of weaker isolation. Traits associated with genome‐wide differentiation in allopatry may thus also contribute to isolation in sympatry. We discuss potentially important additional roles for evolutionary history and ecology in shaping variation in the extent hybridization between closely related pairs of subspecies.     

Gene flow across secondary contact zones of the Emys orbicularis complex in the Western Mediterranean and evidence for extinction and re‐introduction of pond turtles on Corsica and Sardinia (Testudines: Emydidae)

European pond turtles represent a phylogeographically deeply structured complex of distinct taxa. Here, we use mitochondrial DNA sequences (cytochrome b gene) and eight polymorphic microsatellite loci to investigate genetic differentiation and gene flow of Sicilian, Corsican and Sardinian pond turtles and of subspecies involved in two secondary contact zones in the Pyrenean region and Southern Italy. Mitochondrial and microsatellite differentiation is largely concordant in populations from the core regions of the distribution ranges of the studied taxa. Both marker systems provide no evidence for gene flow between Sicilian pond turtles (Emys trinacris) and Southern Italian subspecies of E. orbicularis. By contrast, in the contact zones limited gene flow occurs between distinct subspecies of E. orbicularis. Although the Southern Italian contact zone is significantly older than the Pyrenean contact zone of Holocene age, patterns of asymmetric introgression are similar. Introgressive hybridization leads to the exchange of mitochondria, but microsatellite data indicate only a few individuals with mixed ancestry. This suggests that incipient isolating mechanisms maintain largely discrete nuclear genomic gene pools. Furthermore, this implies that Southern Italy acted as a hotspot rather than as a melting pot of genetic diversity during the last glacial. Pond turtles from Corsica and Sardinia are not differentiated from continental populations of the subspecies E. o. galloitalica, neither in the mitochondrial nor in the quickly evolving microsatellite markers. As the fossil record argues for a continuous presence of pond turtles on both islands since the Middle Pleistocene, this suggests that the native island populations became extinct and the extant turtles were later introduced by prehistoric settlers. The lack of genetic differentiation of pond turtles from Corsica and Sardinia supports the view that the subspecies described from these islands are not valid.     

New evidence for hybrid zones of forest and savanna elephants in Central and West Africa

The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants, and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern Democratic Republic of Congo (DRC). Here, we present new genetic data on hybridization from previously unsampled areas of Africa. Novel statistical methods applied to these data identify 46 hybrid samples – many more than have been previously identified – only two of which are from the Garamba region. The remaining 44 are from three other geographically distinct locations: a major hybrid zone along the border of the DRC and Uganda, a second potential hybrid zone in Central African Republic and a smaller fraction of hybrids in the Pendjari–Arli complex of West Africa. Most of the hybrids show evidence of interbreeding over more than one generation, demonstrating that hybrids are fertile. Mitochondrial and Y chromosome data demonstrate that the hybridization is bidirectional, involving males and females from both subspecies. We hypothesize that the hybrid zones may have been facilitated by poaching and habitat modification. The localized geography and rarity of hybrid zones, their possible facilitation from human pressures, and the high divergence and genetic distinctness of forest and savanna elephants throughout their ranges, are consistent with calls for separate species classification.     

Influence of niche similarity on hybridization between Myriophyllum sibiricum and M. spicatum

The impact of ecological factors on natural hybridization is of widespread interest. Here, we asked whether climate niche influences hybridization between the two closely related plant species Myriophyllum sibiricum and M. spicatum. Eight microsatellite loci and two chloroplast fragments were used to investigate the occurrence of hybridization between these two species in two co‐occurring regions: north‐east China (NEC) and the Qinghai‐Tibetan Plateau (QTP). The climate niches of the species were quantified by principal component analysis with bioclimatic data, and niche comparisons were performed between the two species in each region. Reciprocal hybridization was observed, and M. sibiricum was favoured as the maternal species. Furthermore, hybrids were rare in NEC but common in the QTP. Accordingly, in NEC, the two species were climatically distinct, and hybrids only occurred in the narrow geographical or ecological transition zone, whereas in the QTP, obvious niche overlaps were found for the two species, and hybrids occurred in multiple contact zones. This association between hybridization pattern and climate niche similarity suggests that the level of hybridization was promoted by niche overlap. Compared with the parental species, similar climate niches were found for the hybrid populations in the QTP, indicating that other environmental factors rather than climate were important for hybrid persistence. Our findings highlight the significance of climate niche with respect to hybridization patterns in plants.     

Psocoptera of the Mascarene Islands

Analysis of the known and recently discovered differentiation patterns of 58 forest butterfly species (of the total 66) in the tribe Heliconiini, including over 300 races and forms, has led to the drawing of a map of core areas for evolution in the group. The majority of these are not isolated by any obvious modern physiogeographic barriers to dispersal of these butterflies, and probably correspond to forest refugia during the two or three most recent Quaternary dry periods. The map is in good accord with the results of similar studies in other groups of animals (forest vertebrates and invertebrates) and in forest trees, but indicates a larger number of significant operative refugia (38) than other analyses. Bases for the understanding of differentiation patterns in polytypic continental species are developed, in accord with the refuge theory and using intensive and extensive data on local monomorphic populations and secondary contact zones between differentiated forms. The known forms discussed include: Dione juno miraculosa Hering, Eueides libitina Staudinger, Heliconius xanthocles explicata Stichel, H. eleuchia (Hewitson) and H. leucadia Bates together with a supplementary revision of the tribe giving information published since 1972. The following new forms are described: Eueides emsleyi sp. n. and nine new subspecies of Heliconius: H. aoede philipi, H. wallacei araguaia, H. pardalinus orteguaza, H.p. butleri, H. hecale australis, H.h. barcanti, H. clysonymus tabaconas, H. congener aquilionaris, H. sapho candidus. Geographical details of the refugia are given in Appendix I, and in Appendix II the heliconians are assigned to the postulated refugia.     

The use of geostatistics and GIS for evolutionary history studies: the case of the nose‐horned viper (Vipera ammodytes) in the Balkan Peninsula

Geostatistics and geographical information system (GIS) procedures are novel techniques helpful for the identification of environmental correlates sustaining contact zones among subspecies or closely related species. In this paper, we tried to infer evolutionary scenarios for Vipera ammodytes across the European part of its distribution area using geostatistics and ecological niche‐based models, hence trying to solve several biogeographical questions that remained unclear after the application of classical morphological tools and genetic analyses. Eleven morphological traits from 871 vipers were analysed with geostatistics and ecological niche‐based modelling. Interpolation by kriging was used to generate surfaces of morphological variation, which were combined with spatial principal components analysis (SPCA). SPCA maps were used to test putative morphological differentiated groups with discriminant function analysis (DFA). Maximum entropy modelling and seven environmental variables were used to identify factors limiting the distribution of groups and areas for the potential occurrence of such groups. Three patterns of morphological variation were observed: a north‐west/south‐west cline, transition zones with steep clines of variation in a west–east arc, and particular character traits that disturbed the general cline. SPCA identified between three and nine putative population groups, of which three were supported by DFA. Areas of potential occurrence of these groups were coherent with the range of the three subspecies of V. ammodytes currently recognized. The distribution of all subspecies was mostly related to precipitation in the driest month. Areas of probable sympatry between subspecies are generally small and restricted. The main patterns of geographic variation of morphological characters for V. ammodytes were similar to the patterns obtained for Vipera latastei and Vipera monticola; the same environmental factors limit the distribution of differentiated groups of vipers in the Balkans and the Iberian Peninsula. The influence of humidity on the variation of morphological traits in spatially separated viper taxa from the two European peninsulas coincides with their phylogenetic relatedness. Geostatistics and GIS procedures were successful in the identification of environmental correlates sustaining contact zones among V. ammodytes subspecies in the Balkans. The same techniques should be applied for studying other parapatric forms and refugia regions. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 651–666.     

1961—2010年中国植被区的气候与林火动态变化

气候、植被和人为活动的变化影响到区域的林火动态．基于生态地理区研究全国尺度上林火动态的变化是科学林火管理的基础．根据中国地面气候资料日值数据,把1961—2010年气温和降水两个气象要素差值到网格点（空间分辨率0.25°×0.25°）,分析中国8个生态地理区森林分布区域的火险期气温和降水量变化,采用Mann-Kendall法分析气候和火动态的变化趋势．结果表明： 1961—2010年,中国森林分布区的平均气温呈现线性上升趋势,但降水量变化趋势不显著,所有生态地理区的火险期平均气温显著增加,中温带半干旱/干旱地区草原区增温最显著,而大部分区域的火险期降水量变化不明显.研究区火灾次数呈现明显的波动性,受害森林面积显著下降.除中温带干旱地区荒漠针叶林区的火灾次数和受害森林面积呈现显著的增加趋势外,其他生态地理区都表现为双峰型变化曲线.     

Natural hybridization among subspecies of <Emphasis Type="Italic">Turnera sidoides</Emphasis> L. (Passifloraceae) revealed by morphological and genetic evidence

Turnera sidoides is a complex of outcrossing, perennial, rhizomatous herbs that is widely distributed in southern South America. Five subspecies are recognized taxonomically based on morphological features and geographical distribution. In certain regions, the areas of distribution of the subspecies overlap partially. In such contact zones, the extent of reproductive barriers among subspecies is still largely unknown, but morphologically intermediate individuals have been found in the field, indicating that hybridization may actually occur between subspecies. Crossability among subspecies of T. sidoides has been shown by experimental studies with cultivated plants, but the mechanisms involved in natural populations are still unknown. To investigate the mechanisms that underlie gene flow within the T. sidoides complex, in this paper we analyze the morphological and genetic variation, as well as the crossability among taxa in a contact zone between subspecies pinnatifida and sidoides, in southeastern Uruguay. Our results constitute the first evidences of ongoing natural hybridization between subspecies of T. sidoides and suggest that, although hybridization may not have been of significance in the early phase of the species differentiation, reticulate evolution is ongoing enhancing the current morphological and genetic variability of the complex.     

GENETIC LEAKAGE AFTER ADAPTIVE AND NONADAPTIVE DIVERGENCE IN THE ENSATINA ESCHSCHOLTZII RING SPECIES

The salamander Ensatina eschscholtzii is an example of a ring species in which extant intermediate stages of terminal forms have a nearly continuous range, offering replicated interactions at several stages of divergence. We employ a greatly expanded allozyme database and individual-based analyses to separate the effects of divergence time and gene flow to evaluate how gradual divergence of populations around the ring contributes to the development of reproductive isolation. Despite the high degree of genetic ( D ≤ 0.39) and ecomorphological divergence observed in secondary contacts around the ring, reproductive isolation or rare hybridization is observed only at the terminus of the ring. Instead, in the secondary contacts sampled around the ring, hybrids are common and reproductively successful, enabling genetic leakage between parental genomes and the potential for genetic merger. Nevertheless, genetic admixture is geographically broad (<100 km) only in contacts between ecomorphologically similar populations (within subspecies). When divergence is accompanied by alternative patterns of adaptive divergence (between subspecies), zones of intergradation are narrower and affect populations only locally (>8 km). Diversification and consequent genetic interactions in Ensatina reveal a continuum between populations, ecological races, and species, where polytypic traits and high genetic differentiation are maintained without reproductive isolation.     

Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications

We studied the intraspecific evolutionary history of the South American Atlantic forest endemic Xiphorhynchusfuscus (Aves: Dendrocolaptidae) to address questions such as: Was the diversification of this bird's populations associated to areas of avian endemism? Which models of speciation (i.e., refuges, river as barriers or geotectonism) explain the diversification within X. fuscus? Does the genetic data support subspecies as independent evolutionary units (species)? We used mitochondrial (n=34) and nuclear (n=68) DNA sequences of X. fuscus to study temporal and spatial relationships within and between populations. We described four main monophyletic lineages that diverged during the Pleistocene. The subspecies taxonomy did not match all the evolutionary lineages; subspecies atlanticus was the only one that represented a monophyletic and isolated lineage. The distribution of these lineages coincided with some areas of endemism for passerines, suggesting that those areas could be regions of biotic differentiation. The ancestor of X. fuscus diverged approximately 3 million years ago from Amazonian taxa and the phylogeographic pattern suggested that X. fuscus radiated from northeastern Brazil. Neither the riverine nor the geotectonic vicariance models are supported as the primary cause for diversification of geographic lineages, but rainforest contractions and expansions (ecological vicariance) can explain most of the spatial divergence observed in this species. Finally, analyses of gene flow and divergence time estimates suggest that the endangered subspecies atlanticus (from northeastern Brazil) can be considered a full species under the general lineage species concept.     

不同生态条件下水稻籼粳交后代亚种分化机制

籼粳交育种已成为国内最重要的育种方法之一,明确籼粳亚种分化机制是指导籼粳交育种的关键.本文用InDel(插入/缺失)和ILP(内含子长度多态性)标记,对在辽宁省和广东省种植并用单粒传法、混合法及系谱法构建的籼粳交(七山占/秋光)F₆代群体进行分析.结果表明: 混合法与单粒传法群体无偏分离,粳型判别值(Dj)集中在40%～60%之间;两地系谱法群体总体偏籼(30%～55%),且广东群体(38%)比辽宁(42%)偏籼,两地群体分布呈显著差异.混合法与单粒传法群体中Dj与重要农艺性状基因区域血缘呈显著正相关;而在系谱法中部分正相关被打破,且两地群体籼粳血缘呈规律性分布.表明人工选择是影响籼粳分化的主要因素,并与自然选择协同作用引起群体偏分离现象;群体中一些重要农艺性状的变化与籼粳分化间存在紧密的关系,这可能是影响籼粳交育种在综合亚种优势上未达到预期效果的关键.     

Hotspots of biotic compositional change in lakes along vast latitudinal transects in northern Canada

Ecotones mark zones of rapid change in ecological structure at various spatial scales. They are believed to be particularly susceptible to shifts caused by environmental transformation, making them key regions for studying the effects of global change. Here, we explored the variation in assemblage structure of aquatic primary producer and consumer communities across latitudinal transects in northeastern North America (Québec‐Labrador) to identify spatial patterns in biodiversity that indicated the location of transition zones across the landscape. We analyzed species richness and the cumulative rate of compositional change (expressed as beta‐diversity) of diatoms and chironomids to detect any abrupt shifts in the rate of spatial taxonomic turnover. We used principal coordinates analysis to estimate community turnover with latitude, then applied piecewise linear regression to assess the position of ecotones. Statistically significant changes in assemblage composition occurred at 52 and 55°N, corresponding to the transition between closed‐ and open‐crown forest, and to the southern onset of the forest tundra (i.e., the forest limit), respectively. The spatial distribution of ecotones was most strongly related to air temperature for chironomids and to vegetation‐ and soil‐related chemical attributes of lake water for diatoms, including dissolved organic carbon content and water color. Lakes at mid‐ to high‐latitudes currently face pressures from rapidly rising temperatures, accompanied by large increases in organic carbon inputs from their catchments, often leading to browning and its associated effects. The biota at the base of food webs in lakes located in transition zones are disproportionately affected by the cascading effects of these multi‐factorial changes, concurrent with pronounced terrestrial greening observed in these regions. Similar patterns of biotic shifts have been observed along alpine aquatic transects, indicating the potential for widespread restructuring of cold, high‐altitude and high‐latitude freshwater communities due to global change.     

Patterns of allozyme and morphological differentiation in the Carex flava complex (Cyperaceae) in Fennoscandiaxs

Allozyme and morphological differentiation patterns within the Carex flava complex in Fennoscandia were described by means of multivariate analyses. As a result of these studies, and considering also data on ecology, distribution and hybridization, the following taxa were recognized: C. flava with no infraspecific taxa, C. lepidocarpa with two subspecies, ssp. lepidocarpa and ssp. jemtlandica, C. demissa with no infraspecific taxa, and C. oederi with three varieties, var. oederi , var. bergrothii , and var. pulchella. Carex lepidocarpa ssp. jemtlandica was allozymically divergent from ssp. lepidocarpa , indicating a long period of isolation of the two subspecies. A poor morphological separation in some localities is apparently due to secondary contacts in connection with recolonization of Fennoscandia after the last ice age, resulting in the formation of fertile hybrids and back-crosses. The subdivision of C. oederi into three varieties is supported by ecological data and it is suggested that they have originated by parallel ecotype formation under similar selective regimes in different areas. However, the varietal limits are not supported by differentiation in neutral (allozyme) characters. A phylogenetic hypothesis was constructed by means of neighbour-joining based allozyme data and it was indicated that C. demissa may be more closely related to C. lepidocarpa than to C. oederi. Previous treatments that have reduced the C. flava complex to one or two species may have been based on inappropriate species concepts, too coarse methods of analysis of morphological data, ignorance of patterns of co-occurrence and hybridization, or a combination of these factors.     

Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality

When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced‐generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.     

Genetic structure of muskrat (Ondatra zibethicus) and its concordance with taxonomy in North America

Extrinsic factors such as physical barriers play an important role in shaping population genetic structure. A reduction in gene flow leading to population structuring may ultimately lead to population divergence. These divergent populations are often considered subspecies. Because genetic differentiation may represent differences between subspecies, patterns of genetic structure should reflect subspecies groupings. In this study, we examine the contemporary population genetic structure of muskrat (n = 331) and assess the relevance of 4 geographically distinct subspecies designations across northern North America using 9 microsatellite loci. We predicted that patterns of gene flow and genetic structure would reflect the described subspecies. We found evidence of genetic differentiation between western and eastern regions, and muskrats from Newfoundland (NF) showed significantly lower genetic diversity than central regions. A strong isolation by distance pattern was also detected within the eastern cluster. Our results did not differentiate Ondatra zibethicus spatulus (northwest) from O. z. albus (central), but they suggest a distinction between O. z. obscurus (NF) and O. z. zibethicus (east). This study highlights the need for more phylogenetic studies in order to better understand intraspecific divergence and the genetic characterization of subspecies.     

Microevolution and taxonomy of European reptiles with particular reference to the grass snake Natrix natrix and the wall lizards Podarcis sicula and P. melisellensis

The grass snake Natrix natrix and the wall lizards Podarcis sicula and P. melisellensis are used as examples to compare the procedure and achievements of the conventional approach to naming subspecies with the use of multivariate morphometries to investigate racial differentiation.
The conventional procedure, which has changed little over the last 50 years, fails to take into account the appropriate evolutionary facts or refer to any abstracted levels of divergence necessary for subspecific recognition. Consequently, the patterns of population differentiation are obscured by the recognition of a large number of rather meaningless subspecies. There is a tendency to section clines into artificial categories and arbitrarily delimit subspecies by physiographic features.
On the other hand, the use of multivariate morphometries reveals the patterns of population differentiation which can be related to geological events and patterns of differentiation in other species and species groups. The nature of 'hybrid' zones and population differentiation enables the relative importance of evolutionary forces such as gene flow, selection and genetic drift to be discussed and provides evidence concerning speciation mechanisms. These techniques also contribute to the discussion regarding the nature of species and provide abstracted and operational criteria for taxonomic decisions.
The difference between the results of multivariate analysis and the conventional approach cannot be explained solely on the basis of choice of characters. Some of the advantages and disadvantages of using multivariate morphometries, as opposed to other modern techniques, for investigating racial affinities are discussed.     

Strikingly variable divergence times inferred across an Amazonian butterfly 'suture zone'

'Suture zones' are areas where hybrid and contact zones of multiple taxa are clustered. Such zones have been regarded as strong evidence for allopatric divergence by proponents of the Pleistocene forest refugia theory, a vicariance hypothesis frequently used to explain diversification in the Amazon basin. A central prediction of the refugia and other vicariance theories is that the taxa should have a common history so that divergence times should be coincident among taxa. A suture zone for Ithomiinae butterflies near Tarapoto, NE Peru, was therefore studied to examine divergence times of taxa in contact across the zone. We sequenced 1619bp of the mitochondrial COI/COII region in 172 individuals of 31 species from across the suture zone. Inferred divergence times differed remarkably, with divergence between some pairs of widespread species (each of which may have two or more subspecies interacting in the zone, as in the genus Melinaea) being considerably less than that between hybridizing subspecies in other genera (for instance in Oleria). Our data therefore strongly refute a simple hypothesis of simultaneous vicariance and suggest that ongoing parapatric or other modes of differentiation in continuous forest may be important in driving diversification in Amazonia.     

Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India

Modern phylogenetic data provide unparalleled ability to test biogeographic paradigms, often suggested by differences in species distribution patterns. However, such approaches have been applied less at regional scales, particularly in Asia. In the absence of such data, we examine if concordance of distributional patterns for phenotypes (subspecies) suggest potential biogeographic barriers for birds in peninsular India. Specifically, we examine climatic and physical factors that might limit phenotype distributions in this region. Various physical, vegetation and climatic barriers were demarcated to identify potential biogeographic units within peninsular India. We then collated occurrence of endemic or disjunctly distributed species and subspecies within these units using published range maps. We also quantified turnover between potential units, allowing us to identify significant biogeographic barriers. Three time‐step climate data (Last Glacial Maxima, mid‐Holocene and present) enabled us to examine differences between these potential biogeographic regions through time. The Palk Straits, followed by the Goa Gap (～ 16°N) and the Godavari River emerged as the major barriers in this region. The Palk Straits and Godavari are physical barriers while Goa Gap appears to be a climate‐mediated ecological divide. Mountain barriers like the Palghat Gap are not the most significant barriers as previously thought. Climatically intermediate regions appeared unstable in the past and showed inconsistent affinities to different geographic units across families. We suggest that relative climatic stability of the wet regions of the southern western Ghats could be responsible for high subspecies endemism here. Our approach provides hypotheses that can be tested with comparative multi‐species phylogeographic data in the future.     

Are subspecies useful in evolutionary and conservation biology?

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.