Article

Cryptic diversity in a widespread North American songbird: Phylogeography of the Brown Creeper (Certhia americana)

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Abstract

The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to ascertain relationships in the genus based on morphology alone. Recent genetic and song structure studies of Eurasian Treecreepers identified cryptic species within Old World Certhia that were previously undescribed using morphological characteristics. Here, we use mtDNA to investigate cryptic diversity and patterns of diversification in the Brown Creeper (Certhia americana), the single described Certhia species in the Americas. Phylogenetic analyses identified six well-supported geographically-structured clades; the basal divergence separates a northern and a southern lineage in the Brown Creeper, likely cryptic species previously characterized as many subspecies. Sympatry is prevalent between clades in western North America, where possible contact zones warrant further investigation. Allopatry appears to be the primary driver of deep phylogeographic structure within the Brown Creeper; however, within clade diversity is highly correlated with the life history traits of the populations that comprise the geographically structured phylogroups.

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... The Brown Creeper (Aves: Certhiidae, Certhia americana ) is widespread throughout North America in mature, old-growth coniferous and mixed coniferousdeciduous forests. Currently considered one biological species (AOU 1983), the Brown Creeper has significant phylogeographic structure in mitochondrial DNA (mtDNA; Manthey et al. 2011) with six well-supported geographically structured clades. The basal divergence, a north-south split, coincides with the largest differences in morphology (overall body size and coloration; Webster 1986), while morphological differences between phylogenetic groups (phylogroups) within the basal lineages are largely clinal (Webster 1986). ...
... The basal divergence, a north-south split, coincides with the largest differences in morphology (overall body size and coloration; Webster 1986), while morphological differences between phylogenetic groups (phylogroups) within the basal lineages are largely clinal (Webster 1986). Parapatry among mtDNA clades is prevalent in western North America (Manthey et al. 2011), where possible contact zones warrant investigation using additional genetic markers to differentiate between introgression through hybridization and sympatry between two distinct noninterbreeding phylogroups. Additionally, the use of multiple markers will help identify processes driving patterns of divergence in the Brown Creeper, as well as investigate whether migration (or lack thereof) is prevalent enough to prevent the effects of genetic drift between isolated populations. ...
... Tissue samples of 70 Brown Creeper individuals were obtained from 10 populations (using individuals from the mtDNA study;Fig. 1;Table S2 , Supporting information ), representing the structured clades recovered in mtDNA analyses (Manthey et al. 2011). These include: Chiapas (A; eight individuals; Central America mtDNA clade), Jalisco (B; seven individuals; Mexico mtDNA clade), Morelos (C; eight individuals; Mexico mtDNA clade), Nuevo Leon (D; eight individuals ; Mexico mtDNA clade), New Brunswick (E; seven individuals; eastern mtDNA clade), Mono County California (F; eight individuals; Pacific mtDNA clade), La Plata County Colorado (G; eight individuals; Rocky Mountain mtDNA clade), Riverside County California (H; eight individuals; Pacific mtDNA clade), Monterrey County California (I; six individuals; Pacific mtDNA clade) and Coconino County Arizona (J; two individuals ; Rocky Mountain mtDNA clade). ...
Article
Lineage, or true 'species', trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene-tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single-locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re-evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent-based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.
... In contrast, a recent study investigating genomic patterns of differentiation between two divergent lineages of Brown Creeper (Certhia americana) did not find biased differentiation of the Z chromosome between lineages, but rather a positive relationship between chromosome size and genetic differentiation (). The two divergent (5% mitochondrial DNA (mtDNA) diver- gence;Manthey et al. 2011a) lineages come into contact in Arizona, although it is unclear exactly where the contact occurs.Marshall (1956)studied the plumage morphology of C. americana in Arizona (USA), where the defining differences between northern and southern forms were coloration of the rump (tawny vs. chestnut, respectively) and coloration of the underparts (white vs. sooty relative to throat color). He found the transition from northern to southern birds between the Santa Catalina Mountains and Huachuca Mountains (Fig. 1; his fig. ...
... Wintering and migrant specimens of the northern form have been collected in southern Arizona, within the distribution of the southern form (Phillips et al. 1964). Previous genetic studies (Manthey et al. 2011aManthey et al. , 2011b) of C. americana have included sparse sampling from Arizona, only including individuals from the Kaibab National Forest surrounding the Grand Canyon (northern lineage) and the Chiricahua Mountains (southern lin- eage; Fig. 1). The lack of genetic sampling across the putative contact zone, a transition in color pattern across multiple mountain ranges, and chromosomal variation in patterns of genetic differentiation in birds suggest that a genomic-level investigation of C. americana in Arizona is needed. ...
... An alternative hypothesis to explain this pattern may be that only recent speciation events exhibit elevated sex chromosome differentiation. Relative to Ficedula flycatchers (Ellegren et al. 2012) and Passerina buntings (Carling and Brumfield 2008), the two Certhia lineages are more divergent based on mitochondrial and nuclear sequence data (Manthey et al. 2011aManthey et al. , 2011b). Under a timesince-speciation scenario, biased genomic introgression (i.e., less on sex chromosomes) may have ceased much earlier in Certhia due to lack of interbreeding between lineages. ...
Article
Sky islands, or montane forest separated by different lowland habitats, are highly fragmented regions that potentially limit gene flow between isolated populations. In the sky islands of the Madrean Archipelago (Arizona, USA), various taxa display different phylogeographic patterns, from unrestricted gene flow among sky islands to complex patterns with multiple distinct lineages. Using genomic-level approaches allows the investigation of differential patterns of gene flow, selection, and genetic differentiation among chromosomes and specific genomic regions between sky island populations. Here, we used thousands of SNPs to investigate the putative contact zone of divergent Brown Creeper (Certhia americana) lineages in the Madrean Archipelago sky islands. We found the two lineages to be completely allopatric (during the breeding season) with a lack of hybridization and gene flow between lineages and no genetic structure among sky islands within lineages. Additionally, the two lineages inhabit different climatic and ecosystem conditions and have many local primary song dialects in the southern Arizona mountain ranges. We identified a positive relationship between genetic differentiation and chromosome size, but the sex chromosome (Z) was not found to be an outlier. Differential patterns of genetic differentiation per chromosome may be explained by genetic drift-possibly in conjunction with non-random mating and non-random gene flow-due to variance in recombination rates among chromosomes.
... High avian diversification rates in the highlands relative to the lowlands (Weir, 2006) and the existence of some congruent patterns of low elevation barriers separating sister taxa in a wide variety of groups (Puebla-Olivares et al., 2008;Sánchez-González et al., 2008;Bonaccorso et al., 2008;Bonaccorso, 2009;Weir, 2009;Barber and Klicka, 2010) supports their role in promoting population differentiation and subsequent speciation. However, in some cases there is a lack of correspondence between genetic and phenotypic divergence (Cortés-Rodríguez et al., 2008;Arbeláez-Cortés et al., 2010;Cadena et al., 2010;Barber and Klicka, 2010;Pérez-Emán et al., 2010;Manthey et al., 2011) and the effects of such barriers are not so evident nor consistent. ...
... The samples corresponding to clade 4 are restricted to CG, so it is not surprising to observe this divergence. The role of the lowlands of the Isthmus of Tehuantepec as a geographical barrier for montane taxa is well known, not only for birds (Pérez-Emán, 2005;Bonaccorso et al., 2008;Cortés-Rodríguez et al., 2008;Sánchez-González et al., 2008;Bonaccorso, 2009;Weir, 2009;Barber and Klicka, 2010;Manthey et al., 2011;González et al., 2011), but also for reptiles (Castoe et al., 2009) and mammals (Sullivan et al., 1997(Sullivan et al., , 2000Arellano et al., 2005;León-Paniagua et al., 2007). According to these studies, the phylogeographic break found in our results confirms the influence of this barrier in isolating Central America from Eastern OAX. ...
... Overall, the divergence time estimates indicate main divergence events took place during the early Pleistocene to the middle Pleistocene. This is in accordance with what was found in other avian taxa (García-Moreno et al., 2004;Milá et al., 2007a;Weir, 2009;Barber and Klicka, 2010;Manthey et al., 2011;González et al., 2011) and highlights the importance of this time period for avian diversification in Middle America. Pleistocene climatic oscillations are commonly invoked as the main factor driving recent avian diversification (Klicka and Zink, 1997;Avise and Walker, 1998;Johnson and Cicero, 2004;Weir and Schluter, 2004;Zink and Klicka, 2006;Weir, 2006). ...
Article
Full-text available
The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.
... However, relatively few have examined genetic variation at multiple loci (sequence-based nuclear loci), which allows for an evaluation of the microevolutionary processes responsible for driving lineage divergence in allopatry and provides a more complete picture of the speciation process (for some recent examples in birds, see:456789). In western North America, the genetic footprint from the Pleistocene shows consistent broad scale biogeographic patterns, where forest-dwelling taxa exhibit phylogenetic splits between Rocky Mountain (RM) and pacific (Sierra Nevada and Cascade Mountains; PAC) regions, including both intra-and interspecific splits in birds101112131415, frogs [16], and mammals [17]. These splits are hypothesized to be the product of isolation in distinct refugia during glacial cycles, followed by expansion into current regions after glacial retreat, often into areas where secondary contact occurs. ...
... A mutation rate range of 2–3.2% divergence per million years (prior range for ND2:2.0610 28 to 3.2610 28 mutations/site/year; from: [11],4546) was applied to the mitochondrial locus, with the nuDNA allowed to scale to this rate. Although mutation rates may vary for a variety of reasons (e.g. ...
... tya 95% HPD) from the northern California population. This time period corresponds with the isolation of southern California mountain ranges by the expansion of the Sonoran and Mohave desert vegetation596061 and is concordant with many mtDNA genetic splits between avian phylogroups in California [11], [62]. Additionally, this is similar to the nuclear pattern found in Certhia americana, in which populations of southern and coastal California showed the strongest genetic isolation in western North America [7]. ...
Article
Full-text available
The Pleistocene glacial cycles left a genetic legacy on taxa throughout the world; however, the persistence of genetic lineages that diverged during these cycles is dependent upon levels of gene flow and introgression. The consequences of secondary contact among taxa may reveal new insights into the history of the Pleistocene's genetic legacy. Here, we use phylogeographic methods, using 20 nuclear loci from regional populations, to infer the consequences of secondary contact following divergence in the Mountain Chickadee (Poecile gambeli). Analysis of nuclear data identified two geographically-structured genetic groups, largely concordant with results from a previous mitochondrial DNA (mtDNA) study. Additionally, the estimated multilocus divergence times indicate a Pleistocene divergence, and are highly concordant with mtDNA. The previous mtDNA study showed a paucity of sympatry between clades, while nuclear patterns of gene flow show highly varied patterns between populations. The observed pattern of gene flow, from coalescent-based analyses, indicates southern populations in both clades exhibit little gene flow within or between clades, while northern populations are experiencing higher gene flow within and between clades. If this pattern were to persist, it is possible the historical legacy of Pleistocene divergence may be preserved in the southern populations only, and the northern populations would become a genetically diverse hybrid species.
... Studies on both black (N msat ) or sequenced for mitochondrial control regions (N mt ), allelic richness averaged across loci (Ar), mean number of alleles/locus (A), haplotype diversity (h; mean ± SD), and nucleotide diversity (; mean ± SD). ) and white spruce (Picea glauca (Moench) Voss) found evidence of multiple refugia with at least one in the east and one in the west (Jaramillo-Correa et al. 2004;de Lafontaine et al. 2010), which could help explain the east-west differentiation that we documented in Golden-crowned Kinglets. A number of other continentally distributed avian taxa show an east-west split (Lovette et al. 2004;Bull et al. 2010;Manthey et al. 2011a;Graham and Burg 2012). Thus, it seems likely that the two Golden-crowned Kinglet mitochondrial lineages persisted in isolated areas during the LGM with limited gene flow. ...
... Instead, it appears that, as hypothesized, Golden-crowned Kinglets underwent rapid postglacial differentiation on Haida Gwaii. Similar patterns have been reported in other taxa with comparable geographic distributions (Burg et al. 2005;Bull et al. 2010;Manthey et al. 2011aManthey et al. , 2011bGraham and Burg 2012;Walstrom et al. 2012), suggesting an important role for postglacial divergence in generating contemporary biodiversity of North American taxa. ...
... Current data support the hypothesis that Haida Gwaii Golden-crowned Kinglets are resident year-round and do not migrate seasonally like many other kinglet populations in the north (Ingold and Galati 1997). Sedentary species (McDonald et al. 1999;Coulon et al. 2008;McCormack et al. 2008;Manthey et al. 2011a;Graham and Burg 2012) tend to show higher levels of population structure than migratory species (Ruegg and Smith 2002;Lovette et al. 2004;Boulet and Gibbs 2006), and resident populations of species with mixed migration strategies tend to show increased genetic isolation compared with migratory populations (Boulet and Gibbs 2006;Seki et al. 2007). ...
Article
Full-text available
Relatively recently, temperate regions in North America were covered by extensive ice sheets, making them inhospitable to contemporary flora and fauna. Since the retreat of the ice sheets, these regions have been recolonized by a diversity of taxa, some of which have undergone rapid postglacial divergence. Evidence supports the hypothesis that some taxa persisted in unglaciated refugia during the Last Glacial Maximum, such as on Haida Gwaii (formerly the Queen Charlotte Islands). Many taxa on Haida Gwaii are genetically distinct from mainland populations at neutral molecular markers possibly as the result of isolation in refugia or postglacial colonization. The Golden-crowned Kinglet (Regulus satrapa Lichtenstein, 1823) is a continentally distributed, short-distance migratory passerine inhabiting mature conifer forests including those on Haida Gwaii. We used five microsatellite markers and a 568 base-pair fragment of the mitochondrial control region to determine the likelihood that Haida Gwaii region acted as a refugium for this species during the last ice age. We report significant gene flow between Haida Gwaii and the western North American mainland from mitochondrial markers, but significant population genetic differentiation at nuclear markers. We also report genetic divergence between eastern and western Golden-crowned Kinglets, as well as higher genetic diversity and population substructuring within the western population than within the eastern population. The east–west differentiation probably arose due to isolation in separate Pleistocene refugia south of the ice sheets. However, population differences within the west are likely caused by more recent processes; contemporary differentiation of Haida Gwaii Golden-crowned Kinglets most likely occurred postglacially.
... While many studies have looked at phylogeography in North American birds (e.g. Barrowclough et al. 2004;Burg et al. 2005;), few focus on widespread species (Ball et al. 1988;Colbeck et al. 2008), and fewer still on widespread high-latitude resident species (Klicka et al. 2011). The studies there are tend to lack samples from the northern extent of the range, which is important when evaluating ...
... Gene flow between populations is low as shown by the large number of significant pairwise Φ ST values (Table 2.6). This is similar to the pattern seen in many North American birds (Milot et al. 2000;Bull et al. 2010;Manthey et al. 2011 America is found in both plants (Brunsfeld et al. 2007) and animals (Krosby & Rohwer 2009). In both groups gene flow to other areas is reduced (Tables 2.4 and 2.6, Figure 2.7). ...
... For trees, this may be the fact that dispersing into an established area is difficult as seedlings do not grow well in shade (Johansen & Latta 2003). (Milot et al. 2000;Bull et al. 2010;Manthey et al. 2011) and mammal (Arbogast 2007;Aubry et al. 2009) species. ...
... Patrones con un comportamiento similar se han documentado en muchas otras especies de la región Neotropical. El Istmo de Tehuantepec, la Depresión de Nicaragua, las regiones de baja altitud de Panamá, entre otras no identificadas, son algunas de las barreras biogeográficas que han estimulado profundos eventos de divergencia en América, los cuales comenzaron hace aproximadamente 3.9 a 2.3 millones de años entre las poblaciones de Myioborus miniatus y de otras especies de aves y roedores que habitan los bosques templados de Centro y Suramérica (Bonaccorso 2009;Bonaccorso et al. 2008;García-Moreno et al. 2006;Sanchez et al. 2014;Cadena et al. 2007 Por otra parte, intentar comparar mayores divergencias subespecificas observadas en otras aves y reptiles de México (Delaney et al. 2008;McCormack et al. 2008;Klicka et al. 2011;Manthey et al. 2011;Cortés-Rodríguez et al. 2008;Bryson, García-Vázquez, et al. 2011;Bryson et al. 2012) como Certhia americana (1.3-0.14 millones de años), Apehlocoma califórnica (0.122 millones de años), Aphelocoma ultramarina (1.13-9.35 millones de años), Lampornis amethystinus (5.9 millones de años), Picoides villosus (0.75 millones de años) , Pituophis deppei (1.8 millones de años) y Sceloporus scalaris (7.4-10.1 millones de años), solo permite señalar la razón de estas diferencias, en las distintas características ecológicas y relativa lejanía sistemática con M. m. miniatus, lo cual también es posible traducir en desiguales velocidades de coalescencia, como producto de diferencias en el tamaños efectivo de la población, tasas de mutación, tiempo generacional y heterocigocidad (Avise 1989;Hudson 1990;Arbogast et al. 2002;N A Rosenberg & Nordborg 2002). ...
... Este clado figura una profunda divergencia debido al aislamiento que ejerció la formación de Istmo de Tehuantepec como una barrera biogeográfica, este patrón permite que se identifique a este clado como una especie filogenéticamente distinta. A partir de la evidencia que brindan estos resultados se podría decir que los patrones filogeográficos de Myioborus miniatus se vinculan con la discontinuidad de los bosques templados y los cambios climáticos durante el Cuaternario que sucedieron durante el Pleistoceno Tardío (67,000 a 44,700 años).Sin embargo, la distribución potencial de Myioborus miniatus se prolonga más al norte de la extensión geográfica de este estudio (Figura 15.), es decir, no se incluyeron muestras de las poblaciones que pertenecen a los bosques templados del norte de México, región en la cual se distribuye la subespecie Myioborus miniatus miniatus y donde se han identificado patrones filogeográficos de profunda diversificación subespecifica y de reciente expansión y colonizacion(Cortés-Rodríguez et al. 2008;Klicka et al. 2011;Manthey et al. 2011;Malpica and Ornelas 2014), lo que hace indicar a toda esta región de México como un centro de aguda actividad evolutiva, el cual no ha sido completamente estudiada desde la perspectiva filogeográfica(McCormack et al. 2008). ...
... De esta misma forma pero con una fecha mucho más antigua, el colibrí Lampornis amethystinus presenta una muy antigua divergencia de hace 5.96 millones de años(Cortés-Rodríguez et al. 2008), fecha que coincide casi exactamente con el comienzo de formación del Istmo de Tehuantepec hace 6 millones de años(Barrier et al. 1998). La serpiente Pituophis lineaticollis divergió entre esta barrera hace 1.8 millones de años(Bryson, García-Vázquez, et al. 2011), y con una fecha cercana, Certhia americana presenta esta misma hace 1.32 millones de años(Manthey et al. 2011), Por último, el colibrí Amazilia cyanocephala presenta este mismo aislamiento y divergencia hace apenas entre hace 49 mil a 75 mil años (Rodríguez-Gómez et al. 2013).A pesar de que espacialmente esta congruencia filogeográfica es muy común, temporalmente no lo es, esto se debe a que muy probablemente el Istmo de Tehuantepec, aparte de ser una barrera, también ha llegado a ser por periodos cortos de tiempo, un corredor para los bosques templados, debido a que durante las fases glaciares del Cuaternario estos bosques se pudieron haber expandido en repetidas ocasiones dentro del Istmo y permitido la dispersión episódica de diferentes taxas(Mastretta-Yanes et al. 2015;Rzedowski 1996).Específicamente en M. m. miniatus no se observó una antigua evolución in Situ, a pesar de que muchas especies codistribuidas presentan una diversificación subespecifica con coherencia geográfica entre sus poblaciones. Los chipes Cardellina rubra, Dendroica coronata y Basileuterus belli pertenece a la misma familia que M. m. miniatus, pero a diferencia de esta, Cardellina rubra presenta monófilia recíproca en sus poblaciones que habitan diferentes cordilleras montañosas (SMOc, SMS, EJNV y SMC), mostrando profundas divergencias que van desde hace 1.06-0.47 ...
Thesis
El estudio filogeográfico ha documentado que los eventos geológicos del Plioceno junto a los ciclos glaciares del Cuaternario, tuvieron un papel muy importante en la diversificación biológica de Norteamérica. La especie Myioborus miniatus habita desde el norte de México hasta Argentina, tiene un registro de 12 subespecies a partir de diferencias morfológicas. Un estudio filogeográfico relacionó la variación genética subespecífica con la discontinuidad del hábitat y cambios climáticos durante el Pleistoceno Tardío. Sin embargo, no se integró a la subespecie Myioborus miniatus miniatus. Este trabajo se plantea como propósito deducir el patrón filogeográfico de la subespecie Myioborus miniatus miniatus. A partir de la obtención de 62 secuencias del gen mitocondrial ND2, se realizó un árbol filogenético bayesiano, una red de haplotipos y se obtuvieron los índices de diversidad genética y valores de FST entre las poblaciones. La historia demográfica fue descrita con los índices D de Tajima, F de Fu y valor de regardness, el valor de Tau permitió calcular el tiempo desde que comenzó la expansión. Por último, el tamaño efectivo de la población a través del tiempo fue graficado por medio de un análisis bayesiano Skyline Plot. El análisis filogenético, que incluye todas las subespecies de Myioborus miniatus, indico que M. miniatus miniatus se encuentra en el linaje basal, además, este presenta un nodo bien soportado pero sin monófilia. . La diversidad genética presento un valor alto (0.8909) mientras que la diversidad nucleotidica promedio fue de 0.00191. El análisis de genética de poblaciones indica que no hay estructura genética. En cuanto a la historia demográfica, el análisis Skyline Plot y pruebas de neutralidad indican un escenario de expansión demográfica. A su vez las pruebas de distribución mismatch indican un cambio súbito en el tamaño de la población. En conjunto los resultados indican un incremento del tamaño efectivo de la población durante el último máximo glaciar hace 60 mil años.
... The Brown Creeper (Certhia americana; Aves: Certhiidae) is a common and widespread resident of North American mature, old growth coniferous, and mixed coniferous-deciduous forests. Currently considered a single biological species (AOU 1983, Chesser et al. 2013), the Brown Creeper shows significant genetic structure in both mitochondrial DNA (mtDNA; Manthey et al. 2011a) and nuclear DNA (nDNA; Manthey et al. 2011b). Concordant patterns of genetic structure between datasets identify 3 allopatric lineages: southern (southern Arizona south to Honduras), western (western mountain ranges of the United States and Canada), and eastern (eastern forests of United States and Canada). ...
... The earliest phylogenetic split in the species separates temperate and subtropical populations, coinciding with the largest difference in morphology (overall body size and coloration; Webster 1986), while morphological differences between eastern and western populations are largely clinal. The basal lineages separated~1.50 million years (0.80-3.01 MYA highest probability density [HPD]) ago, while the eastern and western groups within the northern lineage separated 0.6 MYA (0.37-1.23 MYA HPD) ago (Manthey et al. 2011a(Manthey et al. , 2011b. ...
... Population genetic data reveal that gene flow between lineages of Brown Creeper is limited, while gene flow within lineages is prevalent (Manthey et al. 2011a(Manthey et al. , 2011b. Two populations (Monterey County, California, and Sierra Madre Oriental, Mexico) show evidence of population bottlenecks (Manthey et al. 2011a(Manthey et al. , 2011b. ...
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Understanding how distributions of species change through time allows evaluation of hypotheses about factors shaping biogeographic patterns and evolutionary trajectories of genetic lineages. Ideally, such studies would assess whether population genetic processes are associated with geographic distribution shifts, loss or gain of distributional area through time, or fragmentation of distributional areas, information that can now be derived via ecological niche modeling. We examined the distributional changes through time in lineages and populations of Brown Creeper (Certhia americana), a widespread North American bird, to test biogeographic and population genetic hypotheses. In two populations with genetic support for population bottlenecks, Monterey County in California and the Sierra Madre Oriental in Mexico, ecological niche models indicated range contractions and increased fragmentation since the Last Glacial Maximum (LGM). Projections of niche models to the future suggested continuation of range contractions and fragmentation. Of the 3 major allopatric lineages of Brown Creeper (eastern North America, western North America, and southern North America and Central America), the most stable through time was the southern lineage, which corresponds with increased genetic diversity. The potential geographic distribution of the western lineage has remained stable in size but not location since the LGM, corresponding with a genetic signal of isolation by distance. The eastern lineage experienced range contractions during the LGM, likely resulting in the contemporary lack of genetic structure within the lineage. Finally, there is limited evidence of potential range overlap during the LGM between the western lineage and the other 2 lineages, although the overlap is limited to the Arizona sky islands between the west and south lineages. These results suggest that ecological niche modeling and population genetic data may be used as mutual predictors when investigating phylogeographic patterns and processes.
... In contrast to previously studied species, genetic variation in pine siskins north of the isthmus of Tehuantepec reveals a complete lack of structure, even between high latitude populations in the temperate and boreal zones (subspecies pinus) and those in the Mexican highlands (subspecies macropterus). Studies on other avian species have revealed varying degrees of divergence between northern and southern populations, from low levels of divergence involving differences in haplotype frequencies (Milá et al. 2006(Milá et al. , 2007a, to the existence of highly divergent intraspecific lineages (Spellman and Klicka 2006, 2007, Milá et al. 2007b, Manthey et al. 2011, Walstrom et al. 2012, van Els et al. 2014. ...
... Streaked individuals, some similar to S. p. macropterus, have been observed more often in Chiapas than in Guatemala (Vallely et al. 2014), so it is worth asking whether S. p. perplexus in Chiapas share a closer relationship to S. pinus/macropterus. Guatemalan populations cluster with populations from Chiapas in various species examined to date, such as Picoides villosus, , Certhia americana (Manthey et al. 2011) or Ergaticus versicolor (Barrera-Guzmán et al. 2012). Our results from the short sequences obtained from historical museum samples from Chiapas suggest that these individuals belong to the perplexus mtDNA lineage found in Guatemala, rather than to the pinus/macropterus lineage found north of the Isthmus of Tehuantepec, a pattern generally consistent with phenotype. ...
Article
Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin Spinus pinus is a common and widespread songbird showing relative phenotypic uniformity across the North American continent. One exception is the subspecies found in the highlands of northern Central America (S. p. perplexus), which shows marked differentiation in plumage color and shares some traits with the endemic and partly sympatric black-capped siskin S. atriceps, suggesting potential introgression or even a hybrid origin of perplexus. Relationships and species limits among pinus, perplexus and atriceps have been controversial for decades. We provide new molecular evidence to help resolve the evolutionary history of the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron sequences revealed three distinct lineages within the complex, corresponding to: 1) S. pinus individuals from Canada through central Mexico (S. p. pinus and S. p. macropterus), 2) individuals from the highlands of Guatemala and Chiapas (S. p. perplexus), and 3) S. atriceps. Pine siskins across North America show evidence of a recent postglacial population expansion and extremely low levels of diversity and structure. In contrast, S. p. perplexus shows evidence of demographic stasis, reflecting long-term isolation and restricted dispersal. Marked and diagnostic genetic differences among the three lineages in mtDNA and at least one intron, suggest that a hybrid origin of S. p. perplexus is unlikely, yet some degree of introgression between S. p. perplexus and S. atriceps cannot be ruled out in localities where they occur in sympatry.
... Because it is a songbird, sequence data may be BLASTed to the Zebra Finch genome to identify upon which chromosome loci are found. There are two major lineages, split at 32°N latitude, within C. americana identified with both mitochondrial (mtDNA; Manthey et al., 2011a) and nuclear DNA (nDNA; Manthey et al., 2011b). Between the major lineages, there is also apparent quicker differentiation and reduced gene flow on the Z chromosome relative to autosomal loci (Manthey and Spellman, 2014). ...
... Based on these findings, it is likely that there are large amounts of gene flow between western populations of C. americana, precluding nDNA differentiation and exhibiting patterns of mtDNA introgression that formed during periods of allopatry and subsequent contact between mtDNA lineages. In the southern lineage, we identified the same genetic clusters as the previous nDNA study (Manthey et al., 2011b), but were able to obtain strong support for lineage splitting in species tree analyses, where with only 20 loci we were unable to get strong support for relationships between all identified clades. ...
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With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on ~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.Heredity advance online publication, 8 April 2015; doi:10.1038/hdy.2015.27.
... Comparative phylogeographic study of these taxa is the ultimate goal, and common patterns are beginning to emerge. Thus far, studies on White-breasted Nuthatch (Sitta carolinensis;), Mountain Chickadee (Poecile gambeli;) and Brown Creeper (Certhia americana; Manthey et al. 2011) have found significant genetic structure between Rocky Mountain and Sierra Nevada populations of these birds, much like that discerned earlier for Fox Sparrow (Passerella iliaca; Zink 1994) and Blue Grouse (Dendragapus obscurus; Barrowclough et al. 2004). Our preliminary results also suggest that the Peninsular and Transverse ranges of southern California have acted as a refugium for at least some western montane bird species. ...
... Nuthatch (), Mountain Chickadee (), and Brown Creeper (Manthey et al. 2011) along the Great Basin–Sierra Nevada interface. For those species (or species complexes) whose western distribution extends southward into Mexico, recent molecular studies have consistently identified a genetic discontinuity that separates populations associated with montane regions of Mexico from the major mountain ranges in the U.S. Examples include Yellow-eyed and Dark-eyed Junco (Junco phaeonotus, J. hyemalis; Milá et al. 2007a) and Yellow-rumped Warbler (Milá et al. 2007b ). ...
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El carpintero Picoides villosus presenta uno de los ámbitos de distribución reproductiva más amplios entre las aves norteamericanas. Además, es una de las especies más variables morfológicamente, pues comprende hasta 21 subespecies descritas. La amplia distribución y el alto grado de diversidad fenotípica sugieren la existencia de estructura genética subyacente. Utilizamos secuencias del gen ND2 obtenidas de 296 individuos de 89 localidades ubicadas a través del ámbito de distribución de P. villosus para abordar esta pregunta y para explorar la historia evolutiva de la especie. Los análisis filogenéticos identificaron tres clados principales de P. villosus, divergentes entre sí en un 1.5%. Un clado incluyó a las aves de zonas boreales y del este de Norte América (N&E), el segundo a las aves del oeste y suroeste de Norte América (S&W) y el tercero sólo a las aves de una población disyunta de Costa Rica y Panamá. Los análisis de genética poblacional y los modelos de nicho basados en variables climáticas indicaron que los clados del N&E y del S&W han tenido historias evolutivas recientes muy diferentes. Las poblaciones del N&E se caracterizan por la ausencia de estructura genética y por una señal genética de expansión poblacional reciente. En contraste, las poblaciones del S&W están altamente estructuradas y se infiere que su tamaño ha sido estable. Además, el clado del S&W está estructurado en tres grupos adicionales que están aislados geográfica y genéticamente: las montañas de la costa del Pacífico, las montañas del interior y el sur de México. Los patrones de variación genética observados a escala continental sugieren que la topografía compleja de las zonas montañosas del oeste ha tenido una importancia probablemente mayor que la latitud como factor generador de diversidad filogenética dentro de esta especie.
... In both cases it was proposed that northern locations derived from a single refugium, likely in the south. Other species possess a single lineage across eastern North America east of the Rocky Mountains [55][56][57][58], or across all of Canada [59,60]. Samples from the southern portion of the range are required to test whether the species as a whole persisted in a single refugium, or whether there is additional structure in the south, particularly in the southwest, as seen in some of the other sesiid species. ...
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The phylogeographic structure of insect species in North America is poorly understood. The moth family Sesiidae (Lepidoptera) contains many economically important pests of agriculture and forestry, as well as beneficial species used in biological control. Despite their significance, this study constitutes the first broad-ranging population genetic study on North American sesiids. It probes the population structure of eight species of sesiid moths based on sequence variation in cytochrome c oxidase I (N = 191). Haplotype diversity levels were high in seven of the eight species, while nucleotide diversity varied considerably. Patterns ranged from limited structure and a starburst pattern in the raspberry crown borer Pennisetia marginata to highly geographically structured populations in the peachtree borer Synanthedon exitiosa and the maple callus borer Synanthedon acerni. These varied patterns suggest differing evolutionary histories and dispersal abilities. By elucidating population genetic structure and barriers to dispersal we can begin to devise conservation and management plans.
... In order to convert the divergence estimate into time, a divergence rate for ND4 was calibrated using a divergence rate of 1.2% per million years for cytochrome c oxidase subunit I (COI), previously estimated for marine fishes from eight geminate species pairs, including one pair in the genus Lutjanus, distributed across the Isthmus of Panama (Bermingham et al., 1997). Following procedures used in Manthey et al. (2011), the overall mean divergence for both a 652 bp fragment of COI and a 590 bp fragment of ND4 was calculated for a clade of lutjanids that included 48 individuals spread across 23 species. Sequence data were obtained from Gold et al. (2011). ...
Article
Aim Our aim was to assess whether single or multiple vicariance event(s) have occurred in a marine suture-zone in the northern Gulf of Mexico. We estimated the divergence time of two genetically distinct groups of lane snapper (Lutjanus synagris), distributed on either side of this zone, and compared it to the timing of other vicariance events described previously in the area. Location The northern Gulf of Mexico from the Texas coastline to the Atlantic coast of South Florida, USA. The marine suture-zone is proximal to Mobile Bay in Alabama. Methods A Bayesian Markov chain Monte Carlo (MCMC) approach was used to estimate mutation-corrected divergence and genetic migration between eastern and western groups of lane snapper, based on genotypic differences at 13 nuclear-encoded microsatellites obtained previously from 77 and 171 individual samples, respectively. A second estimate of divergence time for eastern and western groups of lane snapper was generated, based on 590 base pairs of DNA sequence from the mitochondrially encoded NADH dehydrogenase subunit 4 (ND4) obtained previously from 45 and 93 individual samples, respectively. Results Both classes of genetic markers (microsatellites and mtDNA) indicated a fairly recent divergence. Confidence intervals for microsatellite-based estimates suggested that divergence began less than 21 thousand years ago (ka), while confidence intervals for mitochondrial DNA-based estimates suggested divergence began less than 130 ka. These estimates were not consistent with vicariance events in the literature, which are hypothesized to have occurred well before 135 ka. Main conclusions These results indicate that the marine suture-zone in the northern Gulf of Mexico features multiple vicariance events and may be characterized by a complex geological/environmental history. We suggest that processes during or after the Wisconsin glaciation (c. 110–18 ka) may have created a previously unrecognized barrier for lane snapper and possibly other species as well.
... In contrast to cyanocephala populations, subspecies guatemalensis did not show evidence of population expansion following the last glaciation. This result is consistent with paleoclimatic data suggesting that environmental conditions varied little in northern Mesoamerica during the ice ages (Lachniet and V azquez-Selem 2005;Caballero et al. 2010), which appoints this region as putative pre-Pleistocene refuge for Nearctic taxa (but see Griscom 1932;Manthey et al. 2011). In particular, the temperate and cloud forests of southern Chiapas and Guatemala show vegetation remnants from the Tertiary (Graham 1998;Ornelas et al. 2010;Aguirre-Planter et al. 2012), indicating that the conditions found today are similar to those during the last episodes of glaciation. ...
Article
The cloud forests of Mesoamerica are highly endangered habitats and the existence of narrowly distributed cryptic endemics will increase the number of taxa at potential risk of extinction. Here, we investigate genetic divergence between populations of the azure-crowned hummingbird (Amazilia cyanocephala), a species complex of endemic hummingbirds to the montane forests of Mesoamerica, by analysing DNA sequences of four mitochondrial markers, morphological data and ecological niche modelling. Our results revealed the presence of two mtDNA lineages corresponding to subspecies A. c. cyanocephala distributed from Tamaulipas to Chiapas in Mexico and Amazilia c. guatemalensis distributed from southern Chiapas to Guatemala. The lineage split can be explained as a consequence of relative isolation of the populations in the different mountain ranges separated by the Motagua-Polochic-Jocotán fault system and corresponds to differences in morphology and to the lack of overlap in environmental space between subspecies. The divergence time estimates do not support the proposed model of a highly constrained temporal window at the end of the Pliocene as divergence at this barrier between cyanocephala and guatemalensis and splits of other bird taxa occurred during the Pleistocene.
... high pre-divergence structure or low postdivergence gene flow on sex chromosomes) lends weight to the hypothesis of the importance of sex chromosomes in the speciation process in Certhia americana. Sampling individuals from a single population for each lineage introduces a potential bias in parameter estimation of gene flow (including potential biases in effective population size estimation); however, this sampling regime limits the effects of genetic structure within each lineage in inducing further biases in IMa, as both the northern and southern lineages of C. americana have strong population structure (Wahlund 1928, Manthey et al. 2011a. ...
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The properties of sex chromosomes, including patterns of inheritance, reduced levels of recombination, and hemizygosity in one of the sexes may result in the faster fixation of new mutations via drift and natural selection. Due to these patterns and processes, the two rules of speciation to describe the genetics of postzygotic isolation, Haldane's rule and the large-X effect, both explicitly include quicker evolution on sex chromosomes relative to autosomes. Because sex-linked mutations may be the first to become fixed in the speciation process, and appear to be due to stronger genetic drift (in birds), we may identify pronounced genetic differentiation in sex chromosomes in taxa experiencing recent speciation and diverging mainly via genetic drift. Here, we use nine sex-linked and 21 autosomal genetic markers to investigate differential divergence and introgression between marker types in Certhia americana. We identified increased levels of genetic differentiation and reduced levels of gene flow on sex chromosomes relative to autosomes. This pattern is similar to those observed in other recently-divergent avian species, providing another case study of the earlier role of sex chromosomes in divergence, relative to autosomes. Additionally, we identify three markers that may be under selection between Certhia americana lineages.
... (2011) found more haplotypes in Mexico; however, only a single ND2 haplotype in Costa Rica and Panama birds and an additional two isolated in multiple southern refugia and recolonized northern areas through multiple colonization routes with subsequent reduction in gene fl ow caused by barriers and behaviour. While Pleistocene glacial cycles have promoted high genetic structure in other sedentary bird species (Barrowclough et al. 2004, Manthey et al. 2011, the high levels of genetic structure for hairy woodpeckers contrasts patterns seen in other sedentary woodpecker species (Ball et al. 1998, Zink et al. 2002, Pulgarin-Restrepo 2011. ...
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Hairy woodpeckers Picoides villosus are a common, year round resident with distinct plumage and morphological variation across North America. We genotyped 335 individuals at six variable microsatellite loci and analyzed 322 mtDNA control region sequences in order to examine the role of contemporary and historical barriers to gene fl ow. In addition we combined genetic analyses with ecological niche modelling to test if hairy woodpeckers were isolated in northern refugia (Alaska, Newfoundland and the Queen Charlotte Islands) during the last glacial maximum. Genetic analyses revealed that gene fl ow among North American hairy woodpecker populations is restricted, but not to the extent predicted for a sedentary species. Populations clustered into two main genetic groups, east and west of the Great Plains in the south and the Rocky Mountains in the north. Contact zones between the two main genetic groups exist in central British Columbia and Washington, but are narrow. Within each group we found additional population structure with genetic breaks between subgroups in the geographic west corresponding to breaks in forested habitat and physical barriers like open expanses of water. Population genetic patterns for hairy woodpeckers have resulted from isolation in multiple southern refugia with the current distribution of genetic groups resulting from post-glacial expansion and subsequent reduction in gene fl ow. While populations in Alaska, Newfoundland and the Queen Charlotte Islands are genetically distinct from other populations, we found no evidence of these areas acting as refugia throughout the Pleistocene. Atlantic Canada populations contained unique haplotypes raising the possibility of a separate colonization from the rest of eastern Canada. Th e endemic subspecies on the island of Newfoundland is not genetically distinct from their closest mainland population unlike the Queen Charlotte Island subspecies.
... For example, the Hairy Woodpecker (Picoides villosus; Klicka et al. 2011, Graham and) exhibits significant genetic differentiation among eastern–boreal and western North American forests. Mountain Chickadees (Poecile gambeli; Spellman et al. 2007) and Brown Creepers (Certhia americana; Manthey et al. 2011) both exhibit strong phylogenetic splits between the Sierra Nevada–Cascade region and the Rocky Mountains–Great Basin region. Dusky Grouse (Dendragapus obscurus) exhibit a phylogenetic split among populations in the Pacific Northwest, Rocky Mountains, and Southwestern forests (Barrowclough et al. 2004). ...
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Climate cycling during the Quaternary played a critical role in the diversification of avian lineages in North America, greatly influencing the genetic characteristics of contemporary populations. To test the hypothesis that North American Northern Goshawks (Accipiter gentilis) were historically isolated within multiple Late Pleistocene refugia, we assessed diversity and population genetic structure as well as migration rates and signatures of historical demography using mitochondrial control-region data. On the basis of sampling from 24 locales, we found that Northern Goshawks were genetically structured across a large portion of their North American range. Long-term population stability, combined with strong genetic differentiation, suggests that Northern Goshawks were historically isolated within at least three refugial populations representing two regions: the Pacific (Cascades–Sierra–Vancouver Island) and the Southwest (Colorado Plateau and Jemez Mountains). By contrast, populations experiencing significant growth were located in the Southeast Alaska–British Columbia, Arizona Sky Islands, Rocky Mountains, Great Lakes, and Appalachian bioregions. In the case of Southeast Alaska–British Columbia, Arizona Sky Islands, and Rocky Mountains, Northern Goshawks likely colonized these regions from surrounding refugia. The near fixation for several endemic haplotypes in the Arizona Sky Island Northern Goshawks (A. g. apache) suggests long-term isolation subsequent to colonization. Likewise, Great Lakes and Appalachian Northern Goshawks differed significantly in haplotype frequencies from most Western Northern Goshawks, which suggests that they, too, experienced long-term isolation prior to a more recent recolonization of eastern U.S. forests.
... The Brown Creeper (Certhia americana) is widely distributed in most forested habitats from Alaska to Nicaragua. Its two main lineages largely evolved in allopatry (Manthey et al. 2011a(Manthey et al. , 2011b(Manthey et al. , 2014 and meet in a microallopatric contact zone in the sky islands-montane forest habitat islands-of Arizona (Marshall 1956;Manthey et al. 2016). We assembled and annotated a chromosome-scale genome for C. americana and resequenced individuals from allopatric and contact zone populations. ...
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The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture-the non-random distribution of functional elements and chromosomal characteristics-through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and micro-chromosomes shapes the genomic signatures of speciation: chromosome size has (1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and (2) a negative relationship with genetic diversity and recombination rate.
... Genetic differentiation observed in Black-capped Chickadees resembles that observed for other forest-dwelling resident North American bird species with broad distributions (Spellman and Klicka 2007;Manthey et al 2011;Burg 2012, Dohms et al. 2017, although see Pulgarín-R. and Burg 2012). Compared with resident species with broad distributions, migratory species appear to exhibit lower levels of population genetic structure (Ball et al. 1988;Milá et al. 2006Milá et al. , 2007Colbeck et al. 2008), although there are exceptions (Milot et al. 2000;Macfarlane et al. 2016). ...
Article
The nonmigratory Black-capped Chickadee (Poecile atricapillus (Linnaeus, 1766)) has a continent-wide distribution extending across large parts of North America. To investigate the phylogeographic structure and verify possible refugia during the last glacial maximum, we sequenced a 678 bp region of the mitochondrial control region from 633 Black-capped Chickadees at 35 sites across North America and performed paleoecological distribution modeling. Two genetically distinct groups were found using multiple analyses: one in Newfoundland (Canada) and a widespread continental group, with additional substructure evident in western continental populations. While gene flow is low throughout the range, it is especially low in peripheral populations. The Newfoundland population has remained isolated from continental populations for at least 65 000 years and contains a number of fixed nucleotide differences. Within the continental populations, Black-capped Chickadees are subdivided into Pacific Coast, Alaska (USA), southeast Rockies, and main-northeast groups consistent with late Pleistocene vicariance events. Evidence of secondary contact was identified between Pacific and main-northeast populations in northwest British Columbia (Canada) and between southeast Rockies and main-northeast groups in Montana (USA). Paleoecological distribution modeling predicted suitable habitat in Alaska, off the coast of Newfoundland, and several locations across the southern United States during the last glacial maximum, whereas suitable habitat during the last interglacial was more similar to the contemporary distribution.
... Populations of these species appear to respond over short distances to variation in climate and habitat quality. This is consistent with the mobility of birds, as shown by dispersal distances of ringed birds recovered away from their natal sites (Sutherland et al. 2000) and the general absence of phylogeographic structure among birds of eastern deciduous forests in North America (Spellman & Klicka 2007;Manthey, Klicka & Spellman 2011). ...
Article
The extent to which populations fill available ecological space is critical to evaluating niche-based theories of community assembly, but habitat suitability for populations is difficult to assess. The absence of a species from areas of otherwise suitable habitat might indicate localized species-specific influences, including biological interactions with competitors, consumers or pathogens, on local population persistence. I used Bray-Curtis ordination axis scores, based on the distributions of forest birds across census plots in eastern North America, as proxies of general features of habitat suitability to predict local abundances of each species of small land bird. I then applied spatial analysis to identify significant spatial structure (Moran's I) in residuals (positive or negative) from predicted local densities, which would indicate localized species-specific influences on population size. Fifty-eight of 79 species exhibited no significant spatial structure in residual abundances, indicating that the ordination axes reflect most of the spatial variation in environmental conditions and habitat characteristics that influence population distribution and density or that samples were too small to detect significant spatial variation. Twenty-one species exhibited significant habitat-independent spatial structure of residuals within distances of 100 km. Aggregations of residuals for these species were independently located, for the most part, and thus probably unrelated to general features of the environment that affect many species. Among factors considered as potential causes of spatial anomalies, positive density dependence (Allee effects), intraspecific social aggregation and area sensitivity in response to forest fragmentation find little support in this analysis. Because of the species-specific nature of these clustered residuals, specialized pathogens are potential candidates to drive spatial anomalies in host abundance.
... The five western subspecies are difficult to differentiate even when using several morphological and plumage traits [35]. Other North American species, such as the Hairy Woodpecker (Picoides villosus), the Brown Creeper (Certhia americana) and the Dark-eyed Junco (Junco hyemalis) present some similarities, for instance, there are several subspecies, and geographic variation in terms of body size and natural history traits [25,28,36]. We studied geographic patterns of genetic variation for the Downy Woodpecker (Picoides pubescens) using a series of population genetic statistics derived from mitochondrial DNA sequences and microsatellite data and created for the first time a species distribution model (SDM) at 21 kya. ...
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The glacial cycles of the Pleistocene have been recognized as important, large-scale historical processes that strongly influenced the demographic patterns and genetic structure of many species. Here we present evidence of a postglacial expansion for the Downy Woodpecker (Picoides pubescens), a common member of the forest bird communities in North America with a continental distribution. DNA sequences from the mitochondrial tRNA-Lys, and ATPase 6 and 8 genes, and microsatellite data from seven variable loci were combined with a species distribution model (SDM) to infer possible historical scenarios for this species after the last glacial maximum. Analyses of Downy Woodpeckers from 23 geographic areas suggested little differentiation, shallow genealogical relationships, and limited population structure across the species' range. Microsatellites, which have higher resolution and are able to detect recent differences, revealed two geographic groups where populations along the eastern edge of the Rocky Mountains (Montana, Utah, Colorado, and southern Alberta) were genetically isolated from the rest of the sampled populations. Mitochondrial DNA, an important marker to detect historical patterns, recovered only one group. However, populations in Idaho and southeast BC contained high haplotype diversity and, in general were characterized by the absence of the most common mtDNA haplotype. The SDM suggested several areas in the southern US as containing suitable Downy Woodpecker habitat during the LGM. The lack of considerable geographic structure and the starburst haplotype network, combined with several population genetic tests, suggest a scenario of demographic expansion during the last part of Pleistocene and early Holocene.
... Most studies have suggested species divergence occurring relatively early during the Pleistocene (Avise et al., 1998a), although mid and late Pleistocene divergence has been shown for North American wolves (~150 kya, Wilson et al., 2000) and sparrow (Spizella) species (~30 kya,). Our results support Pleistocene glacial cycles promoting genetic divergence for hairy woodpeckers with genetic patterns and population structure resembling that found for some other sedentary bird species like the brown creeper (Manthey et al., 2011), but not others like the downy (Ball and Avise, 1992; Zink et al., 2002b) and three toed woodpecker (Zink et al., 2002b). ...
... Molecular data for birds have shown that the effects of the most recent glacial advances (Late Pleistocene) are more often seen within species, in the form of well-marked subspecies and genetically structured populations (Avise and Walker, 1998). For example, phylogeographic surveys of several widely distributed temperate zone birds, such as blue grouse (Dendragapus obscurus; Barrowclough et al., 2004); white-breasted nuthatch (Sitta carolinensis; Spellman and Klicka, 2007); brown creeper (Certhia americana; Manthey et al., 2011), and Swainson's thrush (Catharus ustulatus; Ruegg and Smith, 2002) identify population differentiation that can be attributed to climate change during the recent glacial periods. Current distributions of these species suggest southward displacement and range-size reductions during the late glacial maximum (LGM). ...
... It has also been hypothesized that gene flow among historically isolated groups is occurring in areas of contact between some of these species. The Blue Grouse and Swainson's thrush show evidence for parapatry of mtDNA clades in eastern Oregon and Washington (Ruegg & Smith 2002;Barrowclough et al. 2004), the Brown Creeper shows evidence of sympatry along the western edge of the Great Basin C. americana (Manthey et al. 2011a), and the Hairy Woodpecker shows extensive sympatry across Idaho, Oregon, and Washington (Klicka et al. 2011). However, only a few studies have used multilocus data [AFLP data in the Swainson's Fig. 1 Range map of Sitta carolinensis with subspecies ranges bordered with dotted line. ...
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Inferring the evolutionary and ecological processes that have shaped contemporary species distributions using the geographic distribution of gene lineages is the principal goal of phylogeographic research. Researchers in the field have recognized that inferences made from a single gene, often mitochondrial, can be informative regarding the pattern of diversification but lack conclusive information regarding the evolutionary mechanisms that led to the observed patterns. Here, we use a multilocus (20 loci) data set to explore the evolutionary history of the White-breasted Nuthatch (Sitta carolinensis). A previous single-locus study found S. carolinensis is comprised of four reciprocally monophyletic clades geographically restricted to the pine and oak forests of: (i) eastern North America, (ii) southern Rocky Mountain and Mexican Mountain ranges, (iii) Eastern Sierra Nevada and Northern Rocky Mountains and (iv) Pacific slope of North America. The diversification of the clades was attributed to the fragmentation of North American pine and oak woodlands in the Pliocene with subsequent divergences owing to the Pleistocene glacial cycles. Principal component, clustering and species tree analyses of the multilocus data resolved the same four groups or lineages found in the single-locus study. Coalescent analyses and hypothesis testing of nested isolation and migration models indicate that isolation and not gene flow has been the major evolutionary mechanism responsible for shaping genetic variation, and all the divergence events within S. carolinensis have occurred in response to the Pleistocene glacial cycles.
... Studies on cryptic species throughout the whole tree of life have increased exponentially over the past two decades, fueled in large part by the increasing availability of DNA sequences, which facilitate various genetic approaches to the resolution of cryptic diversity (Sites and Marshall, 2003;Bickford et al., 2007). The prevalence of considerable cryptic diversity has been uncovered in a diverse range of groups, including in plants (Okuyama and Kato, 2009;Carstens and Satler, 2013;Ji et al., 2020;Kinosian et al., 2020;Li et al., 2020) and many animals (Hebert et al., 2004;Oliver et al., 2009;Manthey et al., 2011;Nadler and DE León, 2011;Phiri and Daniels, 2016), suggesting that cryptic species probably represent a significant portion of undiscovered biodiversity (Jörger and Schrödl, 2013;Pante et al., 2015;Loxdale et al., 2016). The ever-increasing cryptic diversity that genetics has resolved poses a taxonomic challenge in terms of what taxonomic ranks should be assigned to cryptic species that can be recognized on a genetic, but not necessarily morphological, basis. ...
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Cryptic species comprise two or more taxa that are grounded under a single name because they are more-or-less indistinguishable morphologically. These species are potentially important for detailed assessments of biodiversity, but there now appear to be many more cryptic species than previously estimated. One taxonomic group likely to contain many cryptic species is Dicranopteris, a genus of forked ferns that occurs commonly along roadsides in Asia. The genus has a complex taxonomical history, and D. linearis has been particularly challenging with many intra-specific taxa dubiously erected to accommodate morphological variation that lacks clear discontinuities. To resolve species boundaries within Dicranopteris, we applied a molecular phylogenetic approach as complementary to morphology. Specifically, we used five chloroplast gene regions (rbcL, atpB, rps4, matK, and trnL-trnF) to generate a well-resolved phylogeny based on 37 samples representing 13 taxa of Dicranopteris, spanning the major distributional area in Asia. The results showed that Dicranopteris consists of ten highly supported clades, and D. linearis is polyphyletic, suggesting cryptic diversity within the species. Further through morphological comparison, we certainly erected Dicranopteris austrosinensis Y.H. Yan & Z.Y. Wei sp. nov. and Dicranopteris baliensis Y.H. Yan & Z.Y. Wei sp. nov. as distinct species and proposed five new combinations. We also inferred that the extant diversity of the genus Dicranopteris may result from relatively recent diversification in the Miocene based on divergence time dating. Overall, our study not only provided additional insights on the Gleicheniaceae tree of life, but also served as a case of integrating molecular and morphological approaches to elucidate cryptic diversity in taxonomically difficult groups.
... These results fail to reject the hypothesis that multiple lineages of M. megacephalus diverged from a common ancestral population and that some or all of these lineages invaded the Great Basin Desert in the early Pleistocene (coincident with the formation of appropriate sandy habitats; see Hafner and Upham 2011 and references therein). Interestingly, this early Pleistocene colonization has been observed in other Great Basin taxa, such as pikas, brown creepers, and mountain chickadees (Grayson 2005;Spellman et al. 2007;Manthey et al. 2011). It is important to note that our IMA estimates of t are significantly more recent than divergence times estimated in previous studies (Hafner et al. 2008;Hafner and Upham 2011). ...
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The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem.
... This correlation between habitat and genetic divergence is common among vireonids (Johnson 1995;Cicero and Johnson 1998;Zwartjes 2001) and other animal species (Carling and Thomassen 2012;Tarroso et al. 2014;Martin et al. 2017;Bell and Irian 2019;MacDonald et al. 2020). Western and eastern populations of warbling vireos likely diversified as the result of isolation in multiple refugia during Pleistocene glaciations (Lovell et al. 2021;Carpenter et al. 2021), a pattern common for other boreal (Weir and Schluter 2004) and temperate species (Johnson and Cicero 2004;Spellman and Klicka 2007;Manthey et al. 2011). This relationship between genetic ancestry and habitat likely reflects different environmental conditions during the Last Glacial Maximum (Avise 2000;Swenson 2006), and postglacial range expansion by both eastern and western warbling vireos likely followed, and were limited by, the recolonization of certain tree species and climate gradients (Williams 2003;Swenson 2006). ...
Article
Following postglacial expansion, secondary contact can occur between genetically distinct lineages. These genetic lineages may be associated with specific habitat or environmental variables and therefore, their distributions in secondary contact could reflect such conditions within these areas. Here we used mtDNA, microsatellite, and morphological data to study three genetically distinct groups of warbling vireo (Vireo gilvus) and investigate the role that elevation and habitat play in their distributions. We studied two main contact zones and within each contact zone, we examined two separate transects. Across the Great Plains contact zone, we found that hybridization between eastern and western groups occurs along a habitat and elevational gradient, whereas hybridization across the Rocky Mountain contact zone was not as closely associated with habitat or elevation. Hybrids in the Great Plains contact zone were more common in transitional areas between deciduous and mixed-wood forests, and at lower elevations (<1000 m). Hybridization patterns were similar along both Great Plains transects indicating that habitat and elevation play a role in hybridization between distinct eastern and western genetic groups. The observed patterns suggest adaptation to different habitats, perhaps originating during isolation in multiple Pleistocene refugia, is facilitating hybridization in areas where habitat types overlap.
... If this split is followed by North American Checklist Committee, it will confuse the lone peninsular record discussed by Pyle and Howell (1993), who tentatively identified their large and dull bird as either P. b. borealis or P. [b.] xanthodryas. Note that xanthodryas twice has been collected in Alaska, but that Gibson and Kessel (1997) Manthey et al. (2011) suggest that Brown Creeper may involve as many as six cryptic species. The most proximal subspecies is zelotes (of the Sierra Nevada-Cascades group), but the actual subspecies and subspecies group involved in BC records remains unknown, and field identification of these groups is poorly understood. ...
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We provide information on 514 native spe-cies we consider documented for the states of Baja California, Baja California Sur, and asso-ciated islands and jurisdictional waters; 225 have been confirmed nesting in the area. The information provided includes occurrence codes, seasonal status, nesting status, and level of documentation. More species, espe-cially nesting species, have been recorded in Baja California (473, 206 confirmed nest-ing) than in Baja California Sur (432, 144). Non-native species and species of hypotheti-cal occurrence are also considered. The role that North American Birds has played in the recording and documentation of these birds is emphasized. We conclude with a discus-sion of some research opportunities among the birds of the peninsula.
... The specific barriers that restrict gene flow will clearly vary among species; however, phylogeographic studies of different species with similar geographic distributions or ecological characteristics allow for more general conclusions about gene flow to be made (i.e., comparative phylogeography; Avise 2000). Well known examples of this comparative approach are the divergences of marine organisms across the Isthmus of Panama (Lessios 2008), and of woodland birds across North America Manthey et al. 2011;Walstrom et al. 2011). In a related approach, comparative phylogeographic studies of species that differ in a key ecological trait, but are otherwise similar, can be used to test whether the key trait influences population differentiation. ...
... Candidates for cryptic species complexes are often concealed within broadly distributed species (Angulo & Icochea, 2010;Florio et al., 2012). In many instances, these species considered to have a wide area of occurrence are in fact a complex of cryptic species (e.g., Lefébure et al., 2007;Manthey, Klicka & Spellman, 2011;Warner, Oppen & Willis, 2015;Dénes et al., 2016). Additionally, specimens of A. platensis from Argentina and Brazil were considered paraphyletic in a study performed by Pérez-Losada et al. (2004), suggesting the presence of a possible species complex. ...
Article
Habitat and taxon-specific properties could affect the propensity for cryptic species to be formed. For example, anomurans of the genus Aegla possess characteristics that suggest the existence of cryptic diversity. The widely distributed species Aegla platensis, besides having been considered paraphyletic, shows a considerable amount of morphological variation in the carapace shape among populations. Thus, the aim of this study was to test the hypothesis that A. platensis encompasses a large complex of cryptic species. Seventeen populations of A. platensis from Argentina and Brazil were analysed using three molecular markers. Contrary to our expectations, 16 populations seem to belong to a single species. Only one population of A. platensis might represent an unrecognized new species. These results are intriguing because they do not fit the phylogeographical pattern seen in other aeglids, which usually have narrow distributions. Although intrinsic characteristics and/or historical biogeographical events could be related to these findings, the factors driving the broad distribution of A. platensis still need to be clarified. Finally, we highlight the fact that taxonomic issues in aeglids are far from being fully understood, and the use of a broad population-based sampling can be useful to improve our understanding of the group's systematics and evolution. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society.
... Candidates for cryptic species complexes are often concealed within broadly distributed species (Angulo & Icochea, 2010;Florio et al., 2012). In many instances, these species considered to have a wide area of occurrence are in fact a complex of cryptic species (e.g., Lefébure et al., 2007;Manthey, Klicka & Spellman, 2011;Warner, Oppen & Willis, 2015;Dénes et al., 2016). Additionally, specimens of A. platensis from Argentina and Brazil were considered paraphyletic in a study performed by Pérez-Losada et al. (2004), suggesting the presence of a possible species complex. ...
Article
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Habitat and taxon-specific properties could affect the propensity for cryptic species to be formed. For example, anomurans of the genus Aegla possess characteristics that suggest the existence of cryptic diversity. The widely distributed species Aegla platensis, besides having been considered paraphyletic, shows a considerable amount of morphological variation in the carapace shape among populations. Thus, the aim of this study was to test the hypothesis that A. platensis encompasses a large complex of cryptic species. Seventeen populations of A. platensis from Argentina and Brazil were analysed using three molecular markers. Contrary to our expectations, 16 populations seem to belong to a single species. Only one population of A. platensis might represent an unrecognized new species. These results are intriguing because they do not fit the phylogeographical pattern seen in other aeglids, which usually have narrow distributions. Although intrinsic characteristics and/or historical biogeographical events could be related to these findings, the factors driving the broad distribution of A. platensis still need to be clarified. Finally, we highlight the fact that taxonomic issues in aeglids are far from being fully understood, and the use of a broad population-based sampling can be useful to improve our understanding of the group's systematics and evolution.
... Sampling (Malaney et al., 2013;Manthey, Klicka, & Spellman, 2011;Spellman & Klicka, 2007) and plants (Gugger, Sugita, & Cavender-Bares, 2010;Potter et al., 2015). MPB from sites in the Great Basin form a lineage unique from MPB in both the Sierra Nevada and Rocky Mountain ranges, similar to what has been found in woodpeckers, which are also a forest-associated species (Klicka, Spellman, Winker, Chua, & Smith, 2011). ...
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Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.
... North American species ( Adams & Burg, 2015;Klicka, Spellman, Winker, Chua, & Smith, 2011;Manthey, Klicka, & Spellman, 2011 , Schonswetter, & Tribsch, 2006;Runck & Cook, 2005). Most notably, congruent patterns of isolation are found in Engelmann and blue spruce ( Ledig et al., 2006), which were restricted to higher elevations and isolated on mountains as aridification occurred in the Great and Wyoming Basins. ...
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An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
... If these unique attributes exist, that would suggest that the population is locally adapted and regionallyshared phenotypic attributes and subtle morphological characteristics have led to the recognition of subspecies (Patten & Unit, 2002;Phillimore & Owens, 2006). It has been argued that genetic assessments of subspecies should focus on putatively adaptive markers rather than neutral markers to distinguish among phenotypes (Patten, 2015; but see Moritz, 1999;Manthey, Klicka, & Spellman, 2011). ...
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The objectives of this study were to describe and evaluate potential drivers of genetic structure in Canadian breeding populations of the Ovenbird, Seiurus aurocapilla. We performed genetic analyses on feather samples of individuals from six study sites using nuclear microsatellites. We also assessed species identity and population genetic structure of quill mites (Acariformes, Syringophilidae). For male Ovenbirds breeding in three study sites, we collected light-level geolocator data to document migratory paths and identify the wintering grounds. We also generated paleohindcast projections from bioclimatic models of Ovenbird distribution to identify potential refugia during the last glacial maximum (LGM, 21,000 years before present) as a factor explaining population genetic structure. Birds breeding in the Cypress Hills (Alberta/Saskatchewan) may be considered a distinct genetic unit, but there was no evidence for genetic differentiation among any other populations. We found relatively strong migratory connectivity in both western and eastern populations, but some evidence of mixing among populations on the wintering grounds. There was also little genetic variation among syringophilid mites from the different Ovenbird populations. These results are consistent with paleohindcast distribution predictions derived from two different global climate models indicating a continuous single LGM refugium, with the possibility of two refugia. Our results suggest that Ovenbird populations breeding in boreal and hemiboreal regions are panmictic, whereas the population breeding in Cypress Hills should be considered a distinct management unit.
... Number of reads, RAD-tags, and coverage are all based on the 75% coverage matrix (Q10) dataset, with the stats for the Q30 dataset in the supplementary information. & Navarro-Sig€ uenza, 2010; Barber & Klicka, 2010; Barrera-Guzm an, Mil a, S anchez-Gonz alez, & Navarro-Sig€ uenza, 2012; Manthey, Klicka, & Spellman, 2011) as well as some woodpeckers (Klicka, Spellman, Winker, Chua, & Smith, 2011) and hummingbirds (Barber & Klicka, 2010; Ornelas et al., 2013 ). In two comparative analyses (Barber & Klicka, 2010; Ornelas et al., 2013 ), including birds, mammals, and plants, diversification across the Isthmus of Tehuantepec occurred within the last two million years, consistent with the recent divergence of Colaptes auratus mexicanoides from more northern populations (based on »1.4% mtDNA sequence divergence). ...
Article
Many species complexes have diversified rapidly and recently, resulting in morphologically diverse populations; however, the rapid pace of diversification often prevents identification of clear phylogeographic structure. Recently, the use of large genomic and reduced-representation genomic datasets has improved resolution of the evolutionary histories in such species and allowed identification of lineages on distinct evolutionary trajectories. The northern flicker (Colaptes auratus) and gilded flicker (Colaptes chrysoides) form a polytypic superspecies group with a complex taxonomic history. The superspecies group includes up to 13 described subspecies, which represent slight geographic variation among five main morphological groups: red-shafted flickers of western North America (cafer group), yellow-shafted flickers of eastern North America (auratus group), Cuban flickers of the Caribbean (chrysocaulosus group), gilded flickers of the U.S. south-west and Mexican north-west (chrysoides group), and Guatemalan flickers of Central America (mexicanoides group). These groups are largely differentiable by variation in feather shaft colour, malar colour, throat colour, crown colour, and back barring. Here, using mitochondrial DNA (mtDNA) and hundreds of single nucleotide polymorphisms (SNPs), we characterized the genetic relationships and genomic distinctiveness of the five morphological groups. We found the mexicanoides group to be the most genetically distinct in both mtDNA (∼1.4% sequence divergence) and large SNP panels. The chrysocaulosus group is differentiated by a single basepair mutation in a small mtDNA fragment. In both mtDNA and SNP panels, there is little genetic distinctiveness between auratus, cafer, and chrysoides morphological groups, with evidence of admixture and a lack of fixed differences.
... The cyt-b clock has been estimated to have an average rate of 2.1% ( 0.1%, 95% CI) divergence/million years (Weir and Schluter 2008). The molecular clock of ND2 has been found to vary among taxa (Lerner et al. 2011, Manthey et al. 2011, and CR sequences have an even greater rate of variation (Zink and Blackwell 1998, Ruokonen and Kvist 2002, Drovetski 2003, Zink and Weckstein 2003. For these reasons, a calibration was deemed necessary for the molecular clock rate of combined ND2 and CR sequences of the white wagtail. ...
... While dispersal of Certhia and Sitta into the New World has not resulted in substantial diver¬ sification (a total of six species by current taxonomy, but possibly as many as 10; Manthey et al, 2011;Walstrom et al., 2012), another certhioid lineage-the ancestor of the wrens and gnatcatchers-dispersed into the New World and diversified both in species number (a total of 106 species; Gill and Donsker, 2017) (Moyle et al., 2016). The continental distribution of each lineage is shown to the right, with black fill indicating presence, and light fill absence. ...
... For instance, the Cascade Range can act as a geographic barrier for gene flow, resulting in genetically distinct clades on either side of the mountains (e.g. Manthey et al. 2011;Walstrom et al. 2012;Rush et al. 2009). Moreover, isolation by distance has also been shown in several other owl species (e.g. ...
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The barn owl (Tyto alba) is a non-migratory species widely distributed across much of North America in areas with extensive old-field and grassland habitat and without extensive winter snow cover. We investigated the genetic diversity and phylogeographic patterns of barn owl populations in western North America, ranging from British Columbia (BC) to southern California, and one eastern population from Pennsylvania. We also determined the genetic distinctiveness of a population off the coast of southern California, Santa Barbara Island, as management plans to control the local owl population are being considered to decrease predation rate on the now threatened Scripps’s Murrelet (Synthliboramphus scrippsi). Using 8 polymorphic microsatellite markers (N = 126) and ND2 mitochondrial sequences (N = 37), we found little to no genetic structure among all sampled regions, with the exception of Santa Barbara Island. The BC mainland population, despite its northwestern geographically peripheral location and ongoing habitat degradation, is not genetically depauperate. However, individuals from Vancouver Island, likewise a peripheral population in BC, exhibited the lowest genetic diversity of all sampled locations. The low global FST value (0.028) estimated from our study suggests that old-field agricultural habitats are well connected in North America. Since the BC population has declined by about 50 % within the last three decades, it is vital to focus on preserving the remaining barn owl habitats in BC to allow successful establishment from neighbouring populations. Additionally, our microsatellite data revealed that the population on Santa Barbara Island showed genetic divergence from its continental counterpart. Mitochondrial data, however, demonstrated that this island population is not a monophyletic lineage containing unique haplotypes, and hence cannot be designated as an Evolutionarily Significant Unit.
... Of particular interest is the widely distributed O. alismoides, which exhibits extensive morphological variation throughout its range. Molecular systematic studies of a diverse range of other groups containing similarly widespread and morphologically variable taxa, including frogs (Angulo and Icochea 2010;Funket al. 2012), lizards (Oliver et al. 2009), birds (Lohman et al. 2010;Manthey et al. 2011) and crabs (Phiri and Daniels 2016), have uncovered evidence of considerable cryptic speciation. Cook and Urmi-König (1984) (Table 1). ...
Article
Ottelia, a pantropical genus of aquatic plants belonging to the family Hydrocharitaceae, includes several narrowly distributed taxa in Asia. Although the Asian species have received comparatively more research attention than congeners in other areas, various key taxonomic questions remain unaddressed, especially with regards to apparent cryptic diversity within O. alismoides, a widespread species complex native to Asia, northern Australia and tropical Africa. Here we test taxonomic concepts and evaluate species boundaries using a phylogenetic framework. We sampled five of the seven species of Ottelia in Asia as well as each species endemic to Africa and Australia; multiple samples of O. alismoides were obtained from across Asia. Phylogenetic trees based on five plastid DNA markers and the nuclear ITS region shared almost identical topologies. A Bayesian coalescent method of species delimitation using the multi-locus data set discerned one species in Africa, one in Australia and four in Asia with the highest probability. The results lead us to infer that a population sampled in Thailand represents a hitherto unrecognised cryptic taxon within the widespread species complex, although the apparent lack of unambiguous diagnostic characters currently precludes formal description. Conversely, no molecular evidence for distinguishing O. cordata and O. emersa was obtained, and so the latter is synonymised under the former. Two accessions that exhibit inconsistent positions among our phylogenetic trees may represent cases of chloroplast capture, however incomplete lineage sorting or polyploidy are alternative hypotheses that ought to be tested using other molecular markers.
... Certainly, a common shortcoming of traditional taxonomic studies based solely on phenetic analysis of morphological variation, is to mistakenly regard as conspecific morphologically similar but genetically (and ultimately evolutionarily) distinct populations (Dayrat, 2005). Such failure to recognise the existence of divergent lineages necessarily results in an underestimation of diversity; a situation to which widespread, morphologically homogeneous species of taxonomically neglected groups are particularly prone (Gill & Kemp, 2002;Goodier et al., 2011;Pyron & Burbrink, 2009;Manthey et al., 2011). ...
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To investigate the presence of cryptic diversity in The African longfin‐tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters–clades that diverge by > 4% and up to 18% (p‐distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.
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Phylogenetic relationships among eight of nine Myrmecocichla chat species were inferred from DNA data. Bayesian posterior probabilities and maximum-likelihood bootstrap percentages strongly supported most branches in the phylogeny. Based on these results, Myrmecocichla, as currently defined, is not monophyletic. The results indicated that Myrmecocichla albifrons is part of a Cercomela + Oenanthe clade, whereas Oenanthe monticola is shown to be a Myrmecocichla. In addition, Myrmecocichla arnotti is shown to be polyphyletic. Phylogenetic analyses support three Southern versus Eastern or Northern speciation events. The dating of these speciation events suggests that they correspond to periods when the Afrotropical forests were expanded to coastal Kenya, 3–5 Mya. This forest expansion thus served as a vicariant driver of speciation in the genus, a result consistent with speciation patterns in other arid-adapted African bird genera. Our haplotype analysis within one of the most widespread and habitat diverse Myrmecocichla species (formicivora, a southern African endemic) showed little genetic variation. Along with speciation patterns shown for Myrmecocichla and other avian genera, this lack of standing variation would appear to support large, inter-regional drivers of speciation as having the largest effect on the diversification of arid-adapted Africa bird species, which is in stark contrast to other vertebrate lineages whose genetic structure often shows strong intra-regional effects.
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We studied the phylogeography and population history of the White Wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of White Wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in Central and South Europe; and clade SE was distributed in Central and East Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of East Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.
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Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson's thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson's thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species' ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
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The distribution of genetic diversity within and among populations in relation to species' geographic ranges is important to understanding processes of evolution, speciation, and biogeography. One hypothesis predicts that natural populations at geographic range margins will have lower genetic diversity relative to those located centrally in species' distributions owing to a link between geographic and environmental marginality; alternatively, genetic variation may be unrelated with geographic marginality via decoupling of geographic and environmental marginality. We investigate the predictivity of geographic patterns of genetic variation based on geographic and environmental marginality using published genetic diversity data for 40 species (insects, plants, birds, mammals, worms). Only about half of species showed positive relationships between geographic and environmental marginality. Three analyses (sign test, multiple linear regression, and meta-analysis of correlation effect sizes) showed a negative relationship between genetic diversity and distance to environmental niche centroid, but no consistent relationship of genetic diversity with distance to geographic range center. This article is protected by copyright. All rights reserved.
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In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi's Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi's Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in the Balkans and is currently widespread, showing strong evidence for population expansion; whereas the other is restricted to Iberia and remained stable. Microsatellites agreed with a genetic break around the Pyrenees, but showed considerable introgression and a weaker genetic structure. Both genetic markers showed an isolation-by-distance pattern associated with the population expansion of the eastern clade. Breeding populations seem to be segregated at the wintering sites, but results on migratory connectivity are preliminary. Savi's Warbler is the only known migratory bird species in which Iberian birds did not expand beyond the Pyrenees after the last glaciation. Despite the long period of independent evolution of western and eastern populations, complete introgression occurred when these groups met in Iberia. Mitochondrial sequences indicated the existence of refugia-within-refugia in the Iberian Peninsula during the last glacial period, which is surprising given the high dispersal capacity of this species. Plumage differences of eastern subspecies seemed to have evolved recently through natural selection, in agreement with the glacial expansion hypothesis. This study supports the great importance of the Iberian Peninsula and its role for the conservation of genetic variation.
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The Hairy Woodpecker (Picoides villosus) has one of the broadest breeding distributions of any North American bird and is also one of the most morphologically variable with as many as 21 described subspecies. This wide distribution and high degree of phenotypic diversity suggests the presence of underlying genetic structure. We used ND2 sequence from 296 individuals from 89 localities throughout the Hairy Woodpecker distribution to address this question and to explore this species' evolutionary history. Phylogenetic analyses identified three main Hairy Woodpecker clades, each ∼1.5% divergent from one another. One clade was comprised of birds from boreal and eastern zones of North America (N&E); the second, of birds from western and southwestern North America (S&W), and the third included only birds from a disjunct population in Costa Rica and Panama. Population genetic analyses and climatic niche models indicated that the N&E and S&W clades have very different recent evolutionary histories. Populations in the N&E are characterized by a lack of genetic structure and a genetic signature of recent population expansion. In contrast, S&W populations are highly structured and relative population stability was inferred. The S&W clade is further structured into three additional geographically and genetically isolated groups: Pacific Coast ranges, interior ranges, and southern Mexico. The continentalscale patterns of genetic variation observed suggest that the complex topography of the montane west has probably been more important than latitude in generating phylogenetic diversity within this species.
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In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
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Two taxa of creepers (Certhia spp.) occur in Europe, C. familiaris and its sibling species C. brachydactyla. The North American Brown Creeper was considered a close relative of C. brachydactyla by one author, a close relative of or conspecific with C familiaris by others, and more recently as a distinct species, C. americana, by the American Ornithologists' Union. Songs of these three creepers are comprised mostly of social calls which are derived from begging calls. Sequence of syllables (syntax) is very conservative in songs of European population of C. familiaris and C. brachydactyla. In contrast, syntax in songs of western North American C. americana is highly variable; however, syllable morphology and syntax in some populations or individuals within populations is remarkably similar to songs of C. brachydactyla, notably from France and Spain. Two social calls and sleeping behaviour of C. americana are also similar to those of C. brachydactyla. Either C. americana and C. brachydactyla are close relatives or they have characters retained from the ancestor common to all three species whereas those in extant C familiaris have diverged.
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We sequenced a part of the mitochondrial cytochrome-b gene from the seven treecreeper species, including 18 subspecies, to reconstruct the phylogeny of the genus Certhia. Species status of all seven species could be affirmed. Certhia discolor, C. himalayana, C. nipalensis, and C. tianquanensis, the species with relatively small distribution ranges in southeast Asia and simple territorial song, are found at the base of all phylogenetic trees, although without good support. A comparatively recent sister species of C. tianquanensis is C. nipalensis, replacing C. discolor as closest relative. Certhia familiaris, C. brachydactyla and C. americana form a derived set of species (again only weak support). The closest relative of C. americana is C. brachydactyla. The C. familiaris subtree is deeply split into two well-defined population groups: a Eurasian group including populations in northern China (Qinling range northward and all Eurasia) and a Sino-Himalayan group (Himalayas and China excluding northern China). In accordance with acoustic characters, the three subspecies hodgsoni, mandellii and khamensis of the Sino-Himalayan group are combined and elevated to species rank: Certhia hodgsoni. Certhia discolor manipurensis is deeply split from nominate discolor as well, and is also promoted to species level. Within C. brachydactyla (western palearctic) and within C. hodgsoni (Himalayas, China) several populations form well-supported separate lineages that diverged quite recently and represent subspecies level. In all other species, molecular–genetic and vocal characters support traditional species delimitation.
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There are many pairs of related western and eastern avian taxa in North America, and for many of these, little is known about their interactions in sympatry. One example is provided by MacGillivray's warblers Oporornis tolmiei and mourning warblers Oporornis philadelphia. There have been occasional reports of range contact and hybridization between these forms, but recent authors have doubted these reports. We show that these two species do in fact come into extensive range contact in the southern Peace Region of British Columbia, just east of the Rocky Mountains. We analyze whether patterns of variation in morphometric traits, eye-arcs, a mitochondrial DNA marker (COI), and a Z-chromosome marker (CHD1Z) are consistent with reproductive isolation or hybridization in this contact zone. Each trait shows strong differences between allopatric MacGillivray's warblers and allopatric mourning warblers, yet in the contact zone there are many birds with a combination of traits typical of both species. This is clearly seen in the molecular markers, for which 18 of 50 birds genotyped in the contact zone have both western and eastern alleles. These patterns strongly indicate the presence of an extensive hybrid zone between MacGillivray's and mourning warblers. Variation in each of the four traits is explained well by a single sigmoidal cline, with a width of roughly 150 km (or 130 km based only on the molecular markers). This is only the fourth hybrid zone known among North American wood-warblers (Parulidae).
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Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (θ) to T and the effect of uncertainty in θ on estimates of population divergence (τ) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on τ decrease when the range over which ancestral population size θ is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time.
Article
For the past two decades, population declines in Neotropical migrant songbirds have been both a flagship conservation issue and the subject of intensive research initiatives. Nonetheless, the design of effective conservation measures for Neotropical migrants has been hindered by a lack of information on where and how migrant populations are regulated. This problem stems in large part from the difficulty of following individual long-distance migrants throughout their annual cycles. As a result, there has been increasing interest in using genetic markers to determine patterns of connectivity between particular breeding populations and overwintering regions. In species with geographically structured genetic variation during the breeding season, genetic markers can be used to determine the origin of migrating and overwintering individuals. This information on demographic connectivity could be then used to infer the locations or seasons contributing to population trends of currently unknown origin. To date, genetic markers (primarily mitochondrial DNA) have been used to survey only a few species of migratory songbirds, with varying success. To provide examples of the geographic scale at which mtDNA markers are likely to prove most relevant to Neotropical migrant conservation, we surveyed breeding-season variation in North American populations of three long-distance migrant taxa: the Yellow-breasted Chat (Icteria virens), Common Yellowthroat (Geothlypis trichas), and Nashville Warbler (Vermivora ruficapilla). We then used this information to screen individuals sampled at overwintering sites in Mexico and Central America. Genetic structure was only found at the broadest continent-wide scale in all three species, which allowed us to assign overwintering individuals to eastern or western breeding lineages but did not allow us to assign overwintering individuals to breeding populations of origin on a finer scale suitable for assaying local demographic trends. Owing to mitochondrial homogeneity among widely separated breeding locations, mtDNA markers (especially when used alone) are unlikely to provide a panacea for the problem of interseasonal connectivity among migrant songbirds. Resumen: En las últimas dos décadas, las declinaciones poblacionales de aves migratorias neotropicales han sido un tema insignia para la conservación así como el objeto de intensas iniciativas de investigación. No obstante, el diseño de medidas de conservación ha estado limitado por la falta de información de dónde y cómo son reguladas las poblaciones migratorias. En gran parte, este problema se deriva de la dificultad de seguir los ciclos anuales de individuos migrantes de larga distancia. En consecuencia, hay un creciente interés en utilizar marcadores genéticos para determinar patrones de conectividad entre determinadas poblaciones reproductivas y sus regiones de hibernación. Los marcadores genéticos pueden ser utilizados para determinar el origen de individuos migrantes e invernantes en especies con variación genética geográficamente estructurada durante la época reproductiva. Esta información sobre conectividad demográfica podría ser utilizada para inferir las localidades o estaciones que contribuyen a las tendencias poblacionales actualmente de origen desconocido. A la fecha, los marcadores genéticos (principalmente ADN mitocondrial) se han utilizado para examinar solo unas cuantas especies de aves migratorias, con éxitos variados. Para proporcionar ejemplos de la escala geográfica en la que los marcadores de ADNmt tienen probabilidad de ser más relevantes para la conservación de migrantes neotropicales, examinamos la variación en la época reproductiva en poblaciones de Norte América de tres taxones migratorios de larga distancia: Icteria virens, Geothlypis trichas y Vermivora ruficapilla. Posteriormente utilizamos esta información para investigar individuos capturados en sitios de hibernación en México y Centroamérica. En las tres especies, la estructura genética se encontró solo en la mayor escala continental, lo que nos permitió asignar a los individuos invernantes a linajes reproductivos orientales u occidentales, pero no nos permitió asignar a los individuos a poblaciones reproductivas de origen en una escala más fina adecuada para analizar tendencias demográficas locales. Debido a la homogeneidad mitocondrial entre localidades reproductivas ampliamente separadas, es poco probable que los marcadores de ADNmt (especialmente cuando se usan solos) sean la panacea para el problema de la conectividad inter-estacional de aves migratorias.