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Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed., (© 2016 The Author(s).)

Our understanding of species phylogeography in much of the Palearctic is incomplete. In addition, many existing studies based solely on mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic history because of the effects of lineage sorting, natural selection, or hybridization. We analyzed 13 introns to assess a mtDNA study of the Eurasian nuthatch (Sitta europaea) that suggested a seemingly contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia. Neutrality tests showed no evidence of selection on either the mtDNA or nuclear sequences. Most nuclear gene trees, except for Z-linked ones, did not recover the three lineages, which we attribute to recent splitting. Analyses of the 13 introns combined revealed the same three groups as did the mtDNA and suggested that nuthatches experienced a trichotomous (or two indistinguishable) split(s) 1-2 million years ago (Mya) and have remained isolated with trifling if not zero gene flow since then, and the Asian group increased in population size. This result demonstrates the usefulness of mtDNA in discovering phylogeographic patterns. The use of multiple nuclear loci facilitated detection of an introgressed individual and improved estimates of process parameters such as divergence time and population expansion. We recommend that phylogeographic studies should be based on both mtDNA and nuclear genes., (© 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.)

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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]

Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, evolutionary species concept to a morphological and distributional data set that resulted in an estimate of 18,043 species of birds worldwide, with a 95% confidence interval of 15,845 to 20,470. In a second, independent analysis, we examined intraspecific genetic data from 437 traditional avian species, finding an average of 2.4 evolutionary units per species, which can be considered proxies for phylogenetic species. Comparing recent lists of species to that used in this study (based primarily on morphology) revealed that taxonomic changes in the past 25 years have led to an increase of only 9%, well below what our results predict. Therefore, our molecular and morphological results suggest that the current taxonomy of birds understimates avian species diversity by at least a factor of two. We suggest that a revised taxonomy that better captures avian species diversity will enhance the quantification and analysis of global patterns of diversity and distribution, as well as provide a more appropriate framework for understanding the evolutionary history of birds. [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]

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]

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]

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]

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]

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

In this article, the authors discuss the study on ZB08 and the significance of nuclear desoxyribonucleic acid (nuDNA) sequences in phylogeography. They note that the study focused on the advantages of sequence data from multiple nuclear loci over mitochondrial sequence. They agree about the significant contributions of nuclear loci to the quantification of population genetic processes.

Abstract: A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ ST-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies. [Copyright &y& Elsevier]