Robert M. Zink

Mitochondrial DNA under siege in avian phylogeography

Mitochondrial DNA (mtDNA) has been the workhorse of research in phylogeography for almost two decades. However, concerns with basing evolutionary interpretations on mtDNA results alone have been voiced since the inception of such studies. Recently, some authors have suggested that the potential problems with mtDNA are so great that inferences about population structure and species limits are unwarranted unless corroborated by other evidence, usually in the form of nuclear gene data. Here we review the relative merits of mitochondrial and nuclear phylogeographical studies, using birds as an exemplar class of organisms. A review of population demographic and genetic theory indicates that mitochondrial and nuclear phylogeographical results ought to concur for both geographically unstructured populations and for populations that have long histories of isolation. However, a relatively common occurrence will be shallow, but geographically structured mtDNA trees—without nuclear gene corroboration—for populations with relatively shorter periods of isolation. This is expected because of the longer coalescence times of nuclear genes (approximately four times that of mtDNA); such cases do not contradict the mtDNA inference of recent isolation and evolutionary divergence. Rather, the nuclear markers are more lagging indicators of changes in population structure. A review of the recent literature on birds reveals the existence of relatively few cases in which nuclear markers contradict mitochondrial markers in a fashion not consistent with coalescent theory. Preliminary information from nuclear genes suggests that mtDNA patterns will prove to be robust indicators of patterns of population history and species limits. At equilibrium, mitochondrial loci are generally a more sensitive indicator of population structure than are nuclear loci, and mitochondrial estimates of FST‐like statistics are generally expected to exceed nuclear ones. Hence, invoking behavioural or ecological explanations of such differences is not parsimonious. Nuclear genes will prove important for quantitative estimates of the depths of haplotype trees, rates of population growth and values of gene flow.

The role of subspecies in obscuring avian biological diversity and misleading conservation policy

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.

Gene flow, refugia, and evolution of geographic variation in the song sparrow (Melospiza melodia)

We surveyed mtDNA restriction‐site variation in song sparrows taken from across their continental range. Despite marked geographic variation in size and plumage color, mtDNA variation was not geographically structured. Subspecies were not identifiable by mtDNA analysis. We suggest that postglaciation dispersal scattered mtDNA haplotypes across the continent, explaining the lack of mtDNA geographic patterns. Evolution of size and plumage coloration has probably proceeded faster than mtDNA evolution, leading to the well‐structured continental pattern of morphological variation. We suggest that the nonordered geographic distribution of haplotypes reflects the recency of population establishment following completion of range expansion. Dispersal distance was estimated from the mtDNA data at 6.1 km per generation, an order of magnitude greater than that (0.3 km) estimated from demographic data. Island samples were not especially different from continental ones. Rooting the haplotype cladogram with a putative primitive haplotype identified Newfoundland and the Queen Charlotte Islands as potential sites of recent refugia. We question whether study of geographic variation in song sparrows leads to insights concerning speciation.

Pleistocene effects on North American songbird evolution

Recent studies have used comparisons of mitochondrial DNA (mtDNA) sequence divergence among populations and species to test existing hypotheses about avian evolution during the Pleistocene epoch. In 1998, Avise and Walker concluded that the Pleistocene was an important time for avian evolution, including the initiation of phylogeographic separations and the completion of speciation events that began in the Pliocene. The study implied that these conclusions conflicted with the study, in 1997, by Klicka and Zink, which concluded that most species pairs previously thought to have originated in the past 250 000 years were much older. The two studies are complementary in the sense that Avise and Walker dealt primarily with phylogeographic (intraspecific) separations. Furthermore, Klicka and Zink concentrated on the inception of divergences whereas the Avise and Walker focused on the timing of the completion of speciation. To accomplish this, Avise and Walker analysed ‘phylogroups’, geographically coherent subsets of biological species in which mtDNA haplotypes exhibit reciprocal monophyly. The study used the average interphylogroup mtDNA distance (0.027), calibrated at 2% per million years, to conclude that speciation required on average one million years to complete. Hence, speciation events begun in the Late Pliocene would have been completed in the mid– to late Pleistocene. Although we appreciate the extended nature of the speciation process and Avise and Walkers insightful attempt to estimate its duration, we conclude that their value was an overestimate by a factor of two. In particular we question whether phylogroups can be used in the novel evolutionary role that Avise and Walker envisioned, because of the vagaries of taxonomic practices and lack of consensus regarding species concepts. To extend their analysis of intraspecific, phylogeographic separations, we compiled previously analysed and newly available data for divergence times for North American songbird (order Passeriformes) phylogroups. More than 80% were initiated at least one million years ago, which is inconsistent with the late Pleistocene origins model previously rejected by Klicka and Zink mentioned above. Although some divergence events can be traced to the late Pleistocene, the significance of the distribution must be judged with reference to a null model. Whether the Pleistocene was a profound time for avian phylogeographic differentiation is at present unknown.

MODES OF SPECIATION IN BIRDS: A TEST OF LYNCH'S METHOD

The view that allopatric speciation is the predominant mode of speciation in animals seems firmly established (Mayr 1942, 1963). Mayr suggested that many species evolve via the establishment of small demes, often peripherally isolated, by dispersal of a few founders from the main body of the range. The view that dispersal is the primary means of achieving allopatry was seriously challenged by the school of vicariance biogeography (Platnick and Nelson 1978). Proponents of this approach suggest that vicariant events fragment ancestral populations and are just as important as, if not more important than, dispersal. Vicariant events are not necessarily expected to cause the isolation of small peripheral populations. Thus, dispersalist and vicariance biogeography predict different frequencies of geographic modes of speciation (Bush 1975), especially in regard to the prevalence of peripheral isolation. Cracraft (1982) studied the geography of speciation among Australian birds and concluded that speciation by vicariance was more common than peripheral isolation. Nevertheless, the frequency of geographic modes of allopatric speciation in birds is not well established. Lynch (1989) hypothesized that the frequency of vicariant, peripheral isolates, and sympatric speciation could be discovered by examining the relative range size and range overlap of sister taxa, either sister species or sister groups. Parapatric speciation, a third form of allopatric speciation (Bush 1975; Endler 1977), was not considered by Lynch because it appears to be phylogenetically indistinguishable from other forms of allopatric speciation (Wiley 1981; Cracraft 1982). In brief, Lynch (1989) suggested that if sister taxa are allopatric and occupy ranges of similar size, their speciation mode is most parsimoniously considered vicariance. If the range

The shifting roles of dispersal and vicariance in biogeography

Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no cladogram was obtained for which all lineages were congruent. Although vicariance was the dominant mode of evolution in these birds, approximately 25% of speciation events could have been derived from dispersal across a pre–existing barrier. An expanded database is now needed to estimate the relative roles of each process. Applying a molecular clock calibration, nearly all speciation events are of the order of a million or more years old, much older than typically presumed.

The causes of mitochondrial DNA gene tree paraphyly in birds.

Gene tree paraphyly is a potentially serious problem because many phylogenetic and phylogeographic studies assume species are monophyletic. Funk and Omland (Funk, D.J., Omland, K.E., 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34, 397-423) found that a seemingly high proportion of bird species (16.7%) were paraphyletic in their mtDNA gene trees. This could imply that mtDNA is an unreliable or even misleading marker for delimiting species. We expand on Funk and Omlands survey and identify the causes of species-level paraphyly in birds. We find that in most cases paraphyly is caused by incorrect taxonomy. In such cases, mtDNA serves systematics by exposing and clarifying taxonomic errors. We find the next most common cause of paraphyly to be incomplete lineage sorting due to recent speciation. Here mtDNA gives a consistent picture of evolution, given the timeframe, but it is not useful for delimiting species and other criteria must be employed. There were relatively few clear instances of paraphyly due to hybridization, though there were more cases where incomplete lineage sorting and hybridization could not be distinguished. We ultimately conclude that, far from a hindrance, mtDNA is generally a useful tool that should continue to facilitate delimitation of avian species.

THE GEOGRAPHY OF MITOCHONDRIAL DNA VARIATION, POPULATION STRUCTURE, HYBRIDIZATION, AND SPECIES LIMITS IN THE FOX SPARROW (PASSERELLA ILIACA )

Geographic variation in mitochondrial DNA (mtDNA) restriction sites was studied in the fox sparrow (Passerella iliaca). Seventy‐eight haplotypes were found. Haplotypes fall into four phylogeographic groups that correspond to groups defined by plumage characters. The geographic distribution of these four groups does not appear congruent with mtDNA patterns in other vertebrates. Within each group, there is little geographic variation in mtDNA restriction sites, although there is geographic variation in plumage coloration and body size. The evolution of mtDNA diversity in fox sparrows seems best explained by vicariant events rather than isolation by distance. The mtDNA evidence suggests that Passerella megarhyncha and Passerella schistacea, two nonsister taxa that occur in western North America, have independently undergone bottlenecks. Hybridization is limited between all pairs of taxa except P. megarhyncha and P. schistacea, where mtDNA evidence suggests a narrow contact zone along the interface of the Great Basin and Sierra Nevada/Cascades. Morphometric characters intergrade over a broader area, suggesting that different processes are responsible for the two gradients. The occurrence of limited backcrossing among taxa suggests that cytoplasmic‐nuclear incompatibility is lacking. The number of biological species would range from one to four, depending on the degree of hybridization tolerated. The mtDNA and plumage characters suggest four phylogenetic species: P. iliaca, P. megarhyncha, P. unalaschcensis, and P. schistacea.

Complex biogeographic history of a Holarctic passerine.

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.

Methods in comparative phylogeography, and their application to studying evolution in the North American Aridlands

Abstract Historical biogeography and comparative phylogeography have much in common. Both seek to discover common historical patterns in the elements of biotas, although typically at different tiers of evolutionary history. Comparative phylogeography is based on phylogeographic analyses of multiple taxa, usually widespread species. By comparing the phylogeographic structures of numerous widespread sympatric species, one can infer whether the current fauna has been historically stable, as evidenced by the relative frequency of geographically congruent reciprocally monophyletic groups. Alternatively, if species distributions are ephemeral over evolutionary time, a mixture of phylogeographic structures is expected. Coalescence analyses contribute information about history irrespective of whether haplotype phylogenies are structured or not. In the aridlands of North America, several isolating events are evident in the phylogeographic patterns of birds, mammals and herps. A mid-peninsular seaway in Baja California, dated at ca. one million years before present, had a pervasive effect, with 13 of 16 assayed species showing a concordant split. Hence, this community appears to have been a stable assemblage of species over the past one million years. In contrast, the avifauna of the Sonoran-Chihuahuan deserts consists of two species with a concordant split and three other species that are undifferentiated across both deserts. Hence, the species in this area have had different histories. The Baja biota appears to resemble its ancestral configuration to a greater degree than the Sonoran-Chihuahuan one. A deeper evolutionary event separated taxa in Baja California from the eastern deserts, showing that the aridlands fauna was affected by events at different times resulting in overlain tiers of history.