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We sequenced the mitochondrial ND2 gene for 290 Bushtits (Psaltriparus minimus) sampled from northern Washington to Guatemala. Phylogenetic analysis sorted specimens into 2 main lineages residing either west (coastal) or east (inland) of the Sierra Nevada and Cascades. These lineages are separated by 3.5% sequence divergence and correspond with the distributions of 2 long-recognized phenotype groupings (brown-capped and plumbeous, respectively). Three additional monophyletic geographically structured lineages were identified. Birds from southmost Baja California (Sierra de la Laguna) segregate from other coastal samples whereas the inland lineage includes additional lineages occurring in southeastern Mexico (Morelos, Puebla, Guerrero, and Oaxaca) plus Guatemala, and southwestern Mexico (Michoacán). Examination of museum specimens revealed that a black-eared phenotype occurs sporadically in the interior lineage in southern U.S. and northern Mexico, increasing in frequency to the south, corresponding roughly with these southern Mexican mtDNA lineages. Degree of sequence divergence between the 2 main lineages suggests a relatively early divergence, and ample time for 2-way introgression to occur. However, only 1 of our sampling localities (Lake Co., Oregon; n = 4) was mixed for coastal (n = 1) and interior (n = 3) lineages suggesting the possibility of reproductive isolation between the 2 main lineages. Secuenciamos el gen mitocondrial ND2 de 290 mitos colectados desde el norte de Washington hasta Guatemala. Los análisis filogenéticos clasificaron a los especímenes en 2 linajes principales que residían ya sea en al oeste (costero) o al este (interior) de la Sierra Nevada y Cascades. Estos linajes se separan por una divergencia de secuencias de 3.5% y corresponden a distribuciones de 2 agrupamientos fenotípicos reconocidos desde hace mucho tiempo (respectivamente capucha marrón y plomizo). Se reconocieron tres linajes adicionales monofiléticos estructurados geográficamente. Aves de la parte más sureña de Baja California (Sierra de la Laguna) se segregan de otras muestras costeras mientras que linajes del interior incluyen otros linajes que se encuentran en el sudeste mexicano (Morelos, Puebla, Guerrero y Oaxaca), sumado a Guatemala y al sudoeste mexicano (Michoacán). La examinación de especímenes de museo reveló que un fenotipo de oreja negra se encuentra esporádicamente en el linaje interior en el sudeste de Estados Unidos y norte de México, que aumenta su frecuencia hacia el sur y corresponde en general con linajes mtADN del sudeste mexicano. El grado de divergencia de secuencias entre los 2 linajes principales sugiere una divergencia relativamente temprana y un tiempo grande para que ocurriera una introgresión de 2 vías. Sin embargo, solo una de las localidades de muestreo (Lake Co., Oregon, n = 4) presentaba una mezcla de linajes costero (n = 1) e interior (n = 3), sugiriendo la posibilidad de aislamiento reproductivo entre los 2 linajes principales. Palabras clave: ADN mitocondrial, árbol genético, divergencia de linaje, filogeografía, modelos de nicho. [ABSTRACT FROM AUTHOR]

Transmissible spongiform encephalopathies (TSEs) are currently incurable, always fatal, and have the potential to cross species boundaries. The expression of TSEs is thought to be influenced by genetic variation at the prion protein gene (PRNP). Although a wide range of mammals exhibit TSEs, it is currently unclear whether they are evolutionarily clustered or if TSE+ species are randomly distributed phylogenetically. We tested whether mammalian species with TSEs are phylogenetically underdispersed on three phylogenetic trees, one constructed from 20 aligned gene sequences for 102 taxa (a species tree), and PRNP gene trees from nucleotide and from amino acid sequence variation. TSEs were present in a variety of orders excluding Chiroptera, Eulipotyphyla, and Lagomorpha, and cetaceans. The occurrence of TSEs on the PRNP and species trees is non-random (Species tree D-value = 0.291; PRNP tree D-value = 0.273; PRNP amino acid tree D-value = 0.238), and TSEs appears to have arisen independently in the recent history of different mammalian groups. We found no evidence that particular protein motifs segregated between species with or without TSEs. Our findings suggest that the evolution of TSEs develops in groups of species irrespective of PRNP genotype. [ABSTRACT FROM AUTHOR]

The timing of migratory passage for sexes and ages of birds is difficult to document because migration is spread out over time and space. We compared sex and age ratios from 10 species of birds that were banded in Wisconsin during fall migration to a sample of autumn window-killed birds from Chicago, Illinois. We assumed that these specimens were a random sample of the migrating population because dates of passage in Wisconsin either predate or were coincident with specimens recovered in Chicago. More juveniles than adults collided with windows, which is expected because of the higher number of juveniles in the fall migratory population. For Connecticut Warbler (Oporornis agilis), Dark-eyed Junco (Junco hyemalis), Ovenbird (Seiurus aurocapilla), and White-throated Sparrow (Zonotrichia albicollis), statistically fewer adults collided with windows than expected. It is possible that adults of these species, who have made at least 2 prior successful migratory journeys, might have experienced some degree of learning to avoid windows. For specimen data, ratios of males to females were approximately equal, except for Swamp Sparrow (Melospiza georgiana; 1:0.82). However, banders were unable to determine sex for a high percentage of each species, ranging from 98.5% undetermined sex for Hermit Thrush (Catharus guttatus) to 48% for Common Yellowthroat (Geothlypis trichas). Taken at face value, banding records for Common Yellowthroat, Dark-eyed Junco, and White-throated Sparrow indicated a much higher percentage of males, whereas for Song Sparrow (Melospiza melodia), females were much more common; 6 species showed no apparent difference in sex ratio between the banding and window samples. In species for which banders declined to identify an individual's sex for a high percentage of birds, we questioned whether the identification of sex in the remaining small percentage was accurate. Thus, we considered the alternative possibility that the specimen data were in fact the most appropriate null hypothesis, and if so, it would suggest that banders have misidentified sexes consistently in 4 species, and ages in 7 species. [ABSTRACT FROM AUTHOR]

A species presence at a particular site can change over time, resulting in temporally dynamic species pools. Ecological niche models provide estimates of species presence at different time intervals. The avifauna of La Brea includes approximately 120 species dating to approximately 15,000 years ago. Niche models predicted presence at the Last Glacial Maximum for over 90% of 89 landbird species. This confirms that niche modeling produces sensible range estimates at the Last Glacial Maximum. For 97 currently local species that are as yet undocumented at La Brea over 90% were predicted to occur; absence is due to insufficient study, lack of the ecological niche, transient occurrence or a behavioral ability to avoid entrapment. Our 366 niche models provide a prospective checklist of the landbird fauna of La Brea. The models indicate fluidity in life history strategies and a higher proportion of resident birds at the LGM (88% to 60%). We evaluated a subset of 103 species in breeding and winter periods using two climate models (MIROC−ESM, CCSM4) with a variety of differing parameters, finding differences in 5% of the niche models. Niche breadths in bark-foraging birds changed little between the present and LGM, suggesting that greater species diversity at the LGM was due to greater niche availability rather than contractions of niche breadths (i.e., niche partitioning). [ABSTRACT FROM AUTHOR]

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos. [ABSTRACT FROM AUTHOR]

The article discusses how hybridization between differentiated taxa can lead to breakdown of accumulated differences between diverging populations. It notes that hybridization was causing the disappearance of a species of tree finch Camarhynchus in the Galapagos Islands. It adds that the phenotypic states of both species at the end of the 30-year study could not have been predicted at the start.

The article presents a study that examined how migratory behavior in birds responded during glacial cycles. Topics discussed include the finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), the proposition that species oscillate between sedentary and migratory strategies with each glacial cycle acting as an adaptive switch.

The article discusses several factors responsible for extinction of the passenger pigeon. Topics discussed include role played by genetic variation in extinction of passenger pigeon; recombination and natural selection led to the highly variable polymorphism distribution of the passenger pigeon genome; and information on effect of natural selection on genetic diversity.

ABSTRACT The trajectory of speciation involves geographic isolation of ancestral populations followed by divergence by natural selection, genetic drift or sexual selection. Once started, the process may experience fits and starts, as sometimes diverging populations intermittently reconnect. In theory populations might cycle between stages of differentiation and never attain species status, a process we refer to as Sisyphean evolution. We argue that the six putative ground finch species (genus Geospiza) of the Galápagos Islands represent a dramatic example of Sisyphean evolution that has been confused with the standard model of speciation. The dynamic environment of the Galápagos, closely spaced islands, and frequent dispersal and introgression have prevented the completion of the speciation process. We suggest that morphological clusters represent locally adapted ecomorphs, which might mimic, and have been confused with, species, but these ecomorphs do not form separate gene pools and are ephemeral in space and time. Thus the pattern of morphological, behavioural and genetic variation supports recognition of a single species of Geospiza, which we suggest should be recognized as Darwin's ground finch ( Geospiza magnirostris). We argue that instead of providing an icon of insular speciation and adaptive radiation, which is featured in nearly every textbook on evolutionary biology, Darwin's ground finch represents a potentially more interesting phenomenon, one of transient morphs trapped in an unpredictable cycle of Sisyphean evolution. Instead of revealing details of the origin of species, the mechanisms underlying the transient occurrence of ecomorphs provide one of the best illustrations of the antagonistic effects of natural selection and introgression. [ABSTRACT FROM AUTHOR]

The Willow Flycatcher (Empidonax traillii) breeds throughout much of the United States, northwestern Mexico, and southeastern and southwestern Canada. A subspecies found in the southwestern United States and northwestern Mexico, E. t. extimus (Southwestern Willow Flycatcher), is listed as endangered under the U.S. Endangered Species Act (ESA). This subspecies was described in 1948, based on comparisons of a few external morphological characters from an unstated number of specimens and localities, although it was excluded from the last official list of subspecies by the American Ornithologists' Union. Like most avian subspecies, its validity has not been tested with modern morphological or genetic methods. Recent assessments of the subspecies have assumed it to be a distinct taxon, and some authors have limited their comparisons to E. t. extimus versus E. t. adastus (the subspecies immediately to the north of E. t. extimus), excluding comparison to western (E. t. brewsteri) and eastern (E. t. traillii) subspecies. To test subspecies limits, I reanalyzed available quantitative data on plumage coloration, and genetic variation in mitochondrial DNA and nuclear loci, and found no support for the distinctiveness of the Southwestern Willow Flycatcher. A test of niche divergence suggested that the Southwestern Willow Flycatcher does not have a significantly different climatic niche from its nearest geographic neighbor, E. t. adastus. I suggest that the Willow Flycatchers of the Southwest represent peripheral populations of an otherwise widespread species that do not merit subspecific recognition, and are therefore inappropriately listed as endangered under the ESA. [ABSTRACT FROM AUTHOR]

[Display omitted] • The plants and animals of the Baja Peninsula include diverse geographic patterns of evolutionary divergence. • The patterns likely stemmed from common events in earth history, such as a mid-peninsular seaway. • We compared phylogenetic analyses of multilocus sequence data to previous studies of mitochondrial and nuclear DNA. • All data sets agree that three species are concordantly differentiated at the Vizcaino Desert, and one species, the California gnatcatcher, shows no geographic differentiation. • The phylogenetic patterns of genetic divergence aid conservation by suggesting areas for reserves, and showing that some subspecies are distinct evolutionary or taxonomic units. Comparative phylogeography explores the historical congruence of co-distributed species to understand the factors that led to their current genetic and phenotypic structures. Even species that span the same biogeographic barrier can exhibit different phylogeographic structures owing to differences in effective population sizes, genetic marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers, including the Vizcaíno Desert and Sierra de la Laguna (Cape District), that have left phylogeographic patterns in some but not all species. We used genome-wide SNP data to test the hypothesis that the diverse phylogeographic patterns inferred from prior studies were supported. We found that mitochondrial DNA, single nuclear gene, and genome-wide SNP data show that the cactus wren and LeConte's thrasher have a concordant historical division at or near the Vizcaíno Desert in north-central Baja California, the Gila woodpecker is at an intermediate stage of divergence, and the California gnatcatcher lacks phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeConte's thrasher. We also analyzed mtDNA data on samples of nine other species that span the Vizcaíno Desert, with four showing no apparent division, and six additional species from the Sierra de la Laguna, all but one of which are differentiated. Reasons for contrasting phylogeographic patterns among these species should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaíno desert is well known in other vertebrate species, and our study further corroborates the extent, profound effect, and importance of this biogeographic boundary. The areas north and south of the Vizcaíno Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation. [ABSTRACT FROM AUTHOR]

Aim A fundamental goal of biogeography is to explain why sister taxa are allopatric. Potential explanations include insufficient time for range expansion, adaptation to allopatrically distributed environments, or ecological similarity that prevents coexistence. Many sister species have been isolated for hundreds of thousands of years, providing ample time to attain sympatry. This focuses attention on the role of ecology. Allopatric phylogroups and phylogenetic sister species often exhibit morphological differences that are apparent responses to differing ecological conditions, revealing a role for ecology in lineage divergence and speciation. However, as Hutchinson proposed five decades ago, a certain level of morphological divergence is typically required before two taxa can partition resources and coexist. This paper uses ecological niche modelling and phylogeography to explore the role of niche divergence in shaping the ranges of sister taxa and in the speciation process. Location Aridlands of North America including the Sonoran and Chihuahuan deserts and Baja California. Methods Ecological niche models were constructed for avian sister phylogroups on either side of two biogeographical barriers: the Vizcaino Desert in Baja California ( c. 28°-30° N), and the Cochise Filter Barrier, which divides the Sonoran and Chihuahuan deserts. Each phylogroup pair was tested for differences in niche identity and niche divergence (using the background test). Results Niche identity can be rejected for each phylogroup, although tests of niche divergence were insignificant. Main conclusions Allopatric sister phylogroups exist in and respond to aspects of different environments, as shown by significant niche identity tests, leading to geographical variation that is often recognized taxonomically, supporting a role for ecology in lineage divergence. However, sister phylogroups also use shared ancestral components of the climatic niche more often than expected by chance, which might prevent selection from yielding divergence in traits related to resource use. Climatic niche divergence does not explain allopatric ranges of phylogroups. Allopatry is maintained because the phylogroups are too similar morphologically, lacking the necessary Hutchinsonian ratios for coexistence. The role of ecology in speciation differs between lineage and biological species concepts owing to their different ranking criteria. [ABSTRACT FROM AUTHOR]

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 (GST = 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. [ABSTRACT FROM AUTHOR]

The study of avian migration has reached sophisticated levels in many areas, including ecology, behaviour, and physiology. Traditional discussions of the evolution of migration, however, have been compromised for several reasons. Previous ideas concerning the ancestral home of migrant species, southern or northern, and whether a partially migratory stage always precedes a fully migratory stage, were not expressed as testable hypotheses. Plotting migratory behaviour on phylogenetic trees has become commonplace and allows tests of traditional hypotheses. Some of these studies are reviewed, lending some support for almost all of the previous ideas. Although phylogenetic mapping helps to frame questions about the evolution of migration in a testable framework, there are two serious issues. First, experimental and observational studies reveal that the expression of migratory behaviour can change rapidly within a lineage, which can violate assumptions of character mapping. In addition, a species distribution model is used to show that current conditions for obligate migratory populations of the chipping sparrow were much restricted at the Last Glacial Maximum, and that the species might have been considered a partial migrant at that time. The expression of migratory behaviour in an extant species might be an artefact of the current inter-glacial period. Only if the rate of gains and losses of migratory behaviour can be incorporated into a phylogenetic mapping exercise will the actual evolutionary pattern of migration be revealed. For example, reconstruction of the ancestral area and the evolutionary history of migratory categories in a clade of New World warblers depended on the assumptions of character state transitions. A second concern is that the trait 'migratory' is too broad for evolutionary analysis and that, if possible, the expression of hyperphagia, Zugunruhe, and navigation could be mapped individually. Loss or suppression of any of these components can lead to sedentary populations, revealing how migratory behaviour can appear and disappear rapidly. A report of low levels of Zugunruhe in a sedentary bird, Saxicola torquata, is reconstructed as derived in a clade of otherwise migratory populations, suggesting that the loss of migration was a result of suppression (but not elimination) of Zugunruhe. When researchers mention the independent origin of migration in a clade, they are most likely referring to the gain or loss of the expression of the ancestral migratory programme, not the de novo evolution of migration per se. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 237-250. [ABSTRACT FROM AUTHOR]

Avian biodiversity is threatened by numerous anthropogenic factors and migratory species are especially at risk. Migrating birds frequently collide with manmade structures and such losses are believed to represent the majority of anthropogenic mortality for North American birds. However, estimates of total collision mortality range across several orders of magnitude and effects on population dynamics remain unknown. Herein, we develop a novel method to assess relative vulnerability to anthropogenic threats, which we demonstrate using 243,103 collision records from 188 species of eastern North American landbirds. After correcting mortality estimates for variation attributable to population size and geographic overlap with potential collision structures, we found that per capita vulnerability to collision with buildings and towers varied over more than four orders of magnitude among species. Species that migrate long distances or at night were much more likely to be killed by collisions than year-round residents or diurnal migrants. However, there was no correlation between relative collision mortality and long-term population trends for these same species. Thus, although millions of North American birds are killed annually by collisions with manmade structures, this source of mortality has no discernible effect on populations. [ABSTRACT FROM AUTHOR]

This article discusses a study which compared molecular markers in the endangered Black-capped Vireo (Vireo atricapilla) and their interpretation in conservation. It provides a review of previous microsatellite analysis of the Black-capped Vireo which revealed a low but statistically significant level of population differentiation with isolation by distance (IBD). Methods and results of the study are described.

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). [ABSTRACT FROM AUTHOR]

Abstract: 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 Omland’s 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. [Copyright &y& Elsevier]

Microsatellites are commonly used molecular markers in phylogeography, and many view them as superior to mitochondrial DNA (mtDNA) gene trees. Being based on frequencies of alleles, and not gene trees, microsatellites exhibit the same analytical drawbacks that resulted in the abandonment of allozymes in genetic studies of population history. I illustrate some these familiar drawbacks by reanalyzing microsatellite data on the song sparrow. Subspecies were previously evaluated with hierarchical analyses of molecular variance, suggesting that subspecies explain 8% of the total variance in microsatellite frequencies. However, this useful heuristic technique only evaluates a priori groupings, and the objective of the study ought to be to discover such groupings, not assume them. In fact, other arbitrary groupings of samples explained the same or greater amounts of variance, and I suggest that for testing subspecies limits, a gene tree is preferable. Grouping population samples by subspecies in the San Francisco Bay area accounts for 1.2% of the microsatellite variation, and despite claims that this informs conservation planning, the data do not support any particular population or subspecies as being genetically or evolutionarily significant. A distance phenogram was used to infer a sequential colonization of the Aleutian Islands, but because individuals were pooled into a priori groups and the phenogram was arbitrarily rooted, this conclusion is tenuous. A plot of heterozygosity vs number of alleles per sample showed that an equally parsimonious interpretation is that current genetic diversity tracks effective population size. Microsatellites should be replaced in nuclear-gene phylogeography by analyses of sequences, which will benefit the study of phylogeography, comparison of nuclear and mtDNA results, and aid in interpreting the results in a conservation context. [ABSTRACT FROM AUTHOR]

Abstract: We explored variation in mitochondrial ND2 gene sequences from 171 stonechats (Saxicola torquata complex) collected from 27 Eurasian and 3 African localities. We found that two widespread neighboring Eurasian subspecies of Siberian stonechat, Saxicola maura maura and S. m. stejnegeri, although very similar in appearance, are not each other’s closest relatives. Eastern Asian S. m. stejnegeri appears to have split from other Palearctic, African, and island stonechats well before differentiation occurred among the latter taxa. Our data indicate that European (S. t. rubicola), central Palearctic (S. m. maura) and eastern Palearctic (S. m. stejnegeri) are independently evolving, and could each warrant separate species status, as assumed earlier for S. rubicola, S. maura and S. torquata. However, we found three localities at which individuals from different major groups occurred. Thus, although these are likely phylogenetic species it is unclear whether they are biological species. There was little phylogeographic structure within the three major Palearctic clades, although samples from Spain might be showing incipient divergence. We maintain that the topology of a mtDNA gene tree is a valid means to discern taxonomic limits. [Copyright &y& Elsevier]

Abstract: DNA sequence data often appear to contradict low-level avian taxonomy, which is usually based on patterns of external phenotypic similarity. We examined such an apparent contradiction in the Nearctic rosy-finches. On the basis of several phenotypic characters the finches were divided into three species congeneric with three Asian species. When Nearctic taxa were analyzed in a principal components analysis, 66.9% of phenotypic variation was explained by differences between the Bering Sea and continental populations, sexual dimorphism and a latitudinal cline. Our phylogenetic analysis of mitochondrial ND2 sequences revealed four clades among six species of rosy-finches. Three clades corresponded to three Asian species. The fourth clade included all three Nearctic species. Their haplotypes were not reciprocally monophyletic and the combined genetic variability of all Nearctic taxa was lower than in two of their Asian congeners. A Z-specific intron (ACO1I9) and an autosomal coding locus (MC1R) provided little additional phylogenetic information, most likely because of the longer coalescence times relative to ND2. Phylogeographic analyses of ND2 data revealed significant gene flow among neighboring localities regardless of their taxonomic assignment. Our analyses showed that DNA and phenotypic data are not in conflict, but rather complement each other, and together help clarify species limits. Our data are consistent with a single species in North America, not three. [Copyright &y& Elsevier]

The article presents an investigation on the microsatellite and mitochondrial DNA (mtDNA) differentiation among the Fox Sparrows. It notes that 46 populations of the Fox Sparrows are observed using five microsatellite loci to determine whether the population assorted into the four groups including the sooty, red, slate-colored and thick-billed Fox Sparrows, which are defined on morphology and mtDNA. The result of principal component analyses showed that the red, sooty, and thick-billed phenotypic-mtDNA groups are differentiated from each other. The four groups qualify as phylogenetic species that shows hybridization and the number of biological species varies on the amount of introgression.

Abstract: Climatic fluctuations during the Quaternary resulted in a dynamic history of species’ range shifts, fragmentations and expansions. Some of these events left traces in the genetic structures of plants and animals. Recent avian phylogeographic studies demonstrated that Holarctic birds responded idiosyncratically to Pleistocene climate fluctuations. We present phylogeographic analyses of the Holarctic collared sand martin (Riparia riparia) and the Asian pale sand martin (Riparia diluta), which were considered conspecific until recently. Mitochondrial and nuclear sequences confirm species status of the pale sand martin; the two species diverged sometime between late Pliocene and middle Pleistocene, but precise dates could not be provided without calibration of the substitution rate. Within the pale sand martin, we found two mitochondrial clades that are likely to have diverged in the Pleistocene, one from Central Siberia, and the other restricted to Mongolia. The two clades were sympatric with the collared sand martin in Buryatiya and Mongolia, respectively. The mitochondrial gene genealogy and φ st analysis of the collared sand martin haplotypes indicate recent, but not ongoing, gene exchange between North America and Eurasia, and restricted gene flow between western and eastern Siberia that likely resulted from historic fragmentation of the species’ range during the last glacial maximum. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

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. [Copyright &y& Elsevier]

The article explains the concept of avian species cited by Remsen. Remsen is an advocate of the biological species concept (BSC). The BSC is not an appropriate framework for studying biodiversity for many reasons. First, Remsen's framework do not consider the phenomnon of reproductive isolation important to the study of interbreeding. Second, BSC provides little basis for judging the species status of alopatric populations. Third, Remsen implied that subspecies can be equated with phylogentic species.

Abstract: 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 Φ 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. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

We compared sequences from two mitochondrial DNA (mtDNA) genes (ND2, ND3) in Savannah Sparrows (Passerculus sandwichensis; n = 112) sampled from Baja California (five sites), coastal Sonora and the continental range (eight sites). Populations from Baja California, San Diego and Sonora formed a clade within which there was no phylogeographic structure; this clade merits species status (Passerculus rostratus). The other clade, consisting of phenotypically "typical" savannah sparrows, should be classified as P. sandwichensis. Among the typical sparrows, there was no phylogeographic structure, although two major clades were discovered. Representatives of each of the two main clades occurred at most sampling localities, excluding Suisan Bay, California and Sable Island, Nova Scotia, Canada. Haplotypes found on Sable Island, representing the "Ipswich Sparrow," were not distinctive, thereby failing to support species status for this taxon. On Isla San Benito, a single haplotype was found, which also occurred in other Mexican localities. The results for Sable Island and Isla San Benito show that size and plumage coloration can evolve rapidly. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

On the basis of plumage coloration and mitochondrial DNA variation, four main groups are recognized within the Fox Sparrow (Passerella iliaca): the red group (iliaca, RE), sooty group (unalaschcensis, SO), thick-billed (megarhyncha, TB), and slate-colored (schistacea, SC). To establish phylogenetic relationships among those four groups, we analyzed 2119 base pairs of sequence from four mitochondrial regions: ND2, ND3, cytochrome b, and control region. The control region is less variable than the coding genes surveyed. Both maximum parsimony and maximum likelihood resolved the same ingroup relationships (RE(SC(TB,SO))). However, placement of the root could not be established, even with four outgroups. Lack of resolution of the root is due to the nearest living relative of the Fox Sparrow being over 11% divergent. Despite lacking a clear root, the data suggest that the two taxa connected by a hybrid zone (TB, SC) are not sister species, which has implications for species limits because under the biological species concept they should be lumped. We recommend that all four main groups be recognized as species. Received 17 January 2001, accepted 14 December 2002. [ABSTRACT FROM AUTHOR]

Using complete cytochrome b sequence data, we determined that the genus Calcarius, as presently recognized, is paraphyletic. Calcarius plus Plectrophenax form a highly supported clade composed of two subclades, a “snow bunting” clade comprised of Plectrophenax plus Calcarius mccownii (formerly in the monotypic genus Rhynchophanes), and a “collared” longspur clade of Calcarius lapponicus, ornatus, and pictus. Contrary to conventional thought, Calcarius is not phylogenetically close to either Calamospiza or Emberiza. Unlike these two genera, the taxonomic affinities of Calcarius appear to lie outside of the sparrow (tribe Emberizini) assemblage. Calcarius appears to be a relatively old songbird lineage, originating between 4.2 and 6.2 million years ago. Within Calcarius, pictus and ornatus form a closely related sister pair (2.9% divergent), as do Calcarius nivalis and hyperboreus (0.18% divergent). The group (Calcarius, sensu lato) is inferred to have its origins at relatively high latitudes in the New World. [Copyright &y& Elsevier]

Provides a framework for understanding avian migration in evolutionary terms by integrating information on the genetics of migration with a macroevolutionary view provided by comparative systematics. Review of the theories on the evolution of avian migration; Components of migration; 'Origin' of migration.

Presents a study which utilized comparative phylogeographic methods to decipher evolutionary responses of terrestrial animals in the North American Aridlands to vicariant events that occurred at different times in the past. Information on the avifauna of the Sonoran-Chihuahuan deserts; Isolating events that are evident in the phylogeographic patterns of birds, mammals and herps; Conclusions.

Discusses the evolutionary history of Darwin's finches. Species of the finches; Difficulty in the classification of the phenotypic variation among the finches; Analysis of the mitochondrial DNA sequences of the birds.

Examines the phylogeographic patterns in the great spotted woodpecker Dendrocopos major acros Eurasia and Japan. Divergence of mitochondrial gene sequences; Evolutionary histories.

Presents a study that compared mitochondrial deoxyribonucleic acid sequences of three-toed woodpeckers within and between Eurasia and North America. Approximate location of sample sites; Methodology; Results of the study.

Examines the distribution of Masked Shrews and Prairie Shrews in Minnesota and examines the possibility of intergradation. Analysis of mitochondrial DNA sequences for shrews; Extent of introgression between the two species; Assessment of the use of morphological characteristics to distinguish the two species.

Presents information on a study which compared mitochondrial DNA sequences for six bird species distributed across the aridlands of North America to document phylogeogaphic patterns and assess levels of congruence. Samples of Canyon Towhees (Pipilo fuscus), Verdins (Auriparus flaviceps) and Black-tailed Gnatcatchers (Polioptila melanura) used in phylogeographic analyses; Methods; Results.

Evaluates four possible explanations that could account for the anomalous lack of mitochondrial DNA differentiation between Zonotrichia (Z.) leucophrys and Z. atricapilla. Accidental amplification of a nuclear pseudogene; Hybrid origin of either Z. leucophrys or Z. atricapilla; Incomplete lineage sorting; Past introgressive hybridization.

Discusses a study which surveyed 1,115 base pairs of mitochondrial DNA sequence from three gene regions in Curve-billed Thrashers. Methods; Results; Discussion on the population history.

The California Gnatcatcher ( Polioptila californica) has become a flagship species in the dispute over development of southern California's unique coastal sage scrub habitat, a fragile, geographically restricted ecosystem with high endemism. One aspect of the controversy concerns the status of the subspecies of this bird in southern California coastal sage scrub that is currently listed as threatened under the U.S. Endangered Species Act. To investigate the recent population history of this species and the genetic distinctiveness of subspecies and to inform conservation planning, we used direct sequencing of mitochondrial DNA (mtDNA) for 64 individuals from 13 samples taken throughout the species' range. We found that coastal sage scrub populations of California Gnatcatchers are not genetically distinct from populations in Baja California, which are dense and continuously distributed throughout the peninsula. Rather, mtDNA sequences from this species contain the signatures of population growth and support a hypothesis of recent expansion of populations from a southern Baja California refugium northward into the southern coastal regions of California. During this expansion, stochastic events led to a reduction in genetic variation in the newly occupied range. Thus, preservation of coastal sage scrub cannot be linked to maintaining the genetic diversity of northern gnatcatcher populations, despite previous recognition of subspecies. Our study suggests that not all currently recognized subspecies are equivalent to evolutionarily significant units and illustrates the danger of focusing conservation efforts for threatened habitats on a single species. [ABSTRACT FROM AUTHOR]

Focuses on a study about the taxonomic status and evolutionary history of Timberline Sparrow or Spizella taverneri, subspecies of Brewer's Sparrow (S. breweri), by comparison of both morphological and molecular characters. Introduction of avian genus Spizella; Discovery of a single, fixed nucleotide difference as basis in distinguishing breweri and taverneri; Suggestion for recognition of taverneri as a specie.

Provides information on a study which examined patterns of variation in skeletal morphometrics, allozymes and mitochondrial DNA restriction sites among species of Toxostoma in the United States. Methodology of the study; Results and discussions of the study; Conclusions.

Focuses on the geographic variations and evolutionary development of birds in North America. What is phylogeography; Related studies; Materials and methods; Results; Discussion.

Examines the dominant mode of speciation in birds using Lynch's method. Lynch's assumption on the role of character evolution in phylogenetic history; Analysis on the phylogenies of 13 lineages of birds; Application of Lynch's method.

Presents results of a restriction site survey of mitochondrial DNA in the fox sparrow (Passerella iliaca), a widespread bird species in North America. Historical genetic patterns of geographic variation in North America; Geographic variation in fox sparrows; Genetic structure of fox sparrows.

Surveys mtDNA restriction-site variation in song sparrows taken from their continental range. MtDNA variation as not geographically structured; Suggestion that postglaciation dispersal scattered mtDNA haplotypes; Evolution of size and plumage coloration; Estimation of Dispersal distance; Potential sites of refugia.