Article

Isolation-driven divergence: Speciation in a widespread North American songbird (Aves: Certhiidae)

Article

Isolation-driven divergence: Speciation in a widespread North American songbird (Aves: Certhiidae)

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Abstract

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.

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... 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.
... Dozens of phylogeographic studies examining variation in mitochondrial DNA have supported the Pleistocene speciation hypothesis and demonstrated the importance of allopatry in promoting lineage divergence in temperate taxa (see [3] for review). 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]. ...
... Second, all sampled populations have similarly high levels of genetic diversity (Fig. 3) with few fixed haplotypes (0–10% of loci fixed) within populations. The observed proportion of fixed haplotypes are low compared to other resident, montane avian species with similar genetic sampling schemes (,20 neutral loci), including Certhia americana (5–45% loci fixed within populations; [7]) and Sitta carolinensis (31–63%; [9]), suggesting that large population sizes have maintained diversity in the Mountain Chickadee. Third, large areas of contiguous suitable climatic niche space (Fig. 6) could have supported many large and interbreeding populations during glacial and interglacial periods. ...
... 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]. The signature of isolated populations in southern California is additionally identified in analyses investigating population sizes. ...
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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.
... Total genomic DNA was previously extracted for earlier studies. The sequences of 21 autosomal loci were obtained from Manthey et al. (2011b), which included anonymous loci (developed in that study) and introns (developed by Backström et al. 2008). An additional nine Z-linked introns were obtained using polymerase chain reaction (PCR) amplification with previously designed primers (Backström et al. 2006, Kimball et al. 2009). ...
... Phased and trimmed haplotype sequences were taken directly from Manthey et al. (2011b) for the autosomal sequences, which were previously checked (and trimmed if necessary) for recombination. Newly sequenced loci were processed using the following methodology. ...
... In total, 3271 base pairs from nine Z-linked loci were sequenced for 16 brown creeper samples and supplemented with 5063 base pairs from 21 autosomal loci from Manthey et al. (2011b). One sample from the data matrix, from the locus MUSK, could not be sequenced. ...
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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.
... 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. ...
... The specific geographic break identified here in C. americana is evident in three other bird species, including the southern range limit of the Mountain Chickadee (Poecile gambeli) and the northern range limit of two species: Mexican Chickadee (Poecile sclateri), and the montane range of the Eastern Bluebird (Sialis sialis). Between C. americana lineages, divergence likely occurred during the Pleistocene (Manthey et al. 2011b); however, during the Pleistocene glacial cycles there is little evidence for increased distributional overlap among lineages during glacial maxima based on ecological niche modeling (), suggesting mechanisms other than climate cycles have restricted gene flow among lineages. ...
... 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.
... With new methods for obtaining reduced-representation libraries of the genome (for example, restriction digest-based methods, Miller et al., 2007 andultraconserved elements, Faircloth et al., 2012) for many individuals, phylogeographic studies may contain thousands of loci with dozens of individuals sampled. In songbirds, strong patterns of interchromosomal synteny (Kawakami et al., 2014), the published genome of the Zebra Finch (Taeniopygia guttata; Warren et al., 2010) and thousands of genetic markers across the genome allow the opportunity to investigate not only phylogeographic structure in a clade well known for its high levels of geographic differentiation (Manthey et al., 2011a), but also diversity and differentiation across chromosomes (Manthey and Spellman, 2014). ...
... 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). ...
... Tissue samples of 41 C. americana individuals were obtained from eight localities ( Figure 1, Table 1, Supplementary Table 1), representing the structured clades recovered in previous mtDNA analyses (Manthey et al., 2011a). Total genomic DNA was extracted from tissue samples using a QIAGEN (Hilden, Germany) DNeasy tissue extraction kit following the manufacturer protocols. ...
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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.
... Western North America is a favored area for phylogeography, because of its relative ease of access to sampling localities, isolation and multitude of biomes, and habitat heterogeneity. These properties have led to studies of a number of widespread species with morphologically, behaviorally or ecologically well-defined subspecies or populations, with several geographically isolated populations across mountain ranges, deserts, coastal scrub, and grasslands (Demboski and Cook, 2001;Nielson et al., 2001;Burns et al., 2007;Milà et al., 2007a;, Gugger et al., 2011, Manthey et al. 2011McCormack et al., 2011;Van Els et al., 2012). The examination of phylogeographic structure in these species has resulted in the observation multiple reciprocally monophyletic mitochondrial DNA (mtDNA) groups (in some cases supported by nuclear DNA), isolated from each other by natural barriers. ...
... However, even if habitat is continuous across the landscape and throughout the distribution of the studied taxon, phylogeographic variation may build up through historic demographic processes. In several western North American taxa, Pleistocene refugia played important roles in the buildup of genetic variation (Barrowclough et al., 2004;Demboski and Cook, 2001;Manthey et al., 2011;Nielson et al., 2001;. These refugia are generally found outside of the current range of the taxa studied (although see Van Els et al., 2012), and in many instances led to isolation of lineages and the resulting accrual of distinct genetic variation. ...
... Current understanding of how geography impacts lineage diversification has been developed in part via studies of avian biodiversity across the globe (Campagna et al., 2015;Irwin et al., 2018;Lovette, 2005;Manthey et al., 2011;Moyle et al., 2009). One key region for studying avian biogeography has been the western Pacific, which, due to its highly fragmented geography, generates ample opportunity for isolation and divergence between incipient lineages (Mayr and Diamond, 2001). ...
Article
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.
... First, the program STRUCTURE (Prichard et al. 2000) was used to determine the number of groups; the individual was the unit of analysis. The 13 nuclear introns were formatted as single-nucleotide polymorphism (SNP) (Manthey et al. 2011;Walstrom et al. 2012). Individuals (n = 60) represented by two or more loci were used; 39 individuals were from the Asian haplogroup in the mtDNA tree, 14 from the European clade, and seven from the Caucasus (Table S1). ...
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Our understanding of species phylogeography in much of the Palearctic is incomplete. In addition, many existing studies based solely on mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic history because of the effects of lineage sorting, natural selection, or hybridization. We analyzed 13 introns to assess a mtDNA study of the Eurasian nuthatch (Sitta europaea) that suggested a seemingly contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia. Neutrality tests showed no evidence of selection on either the mtDNA or nuclear sequences. Most nuclear gene trees, except for Z-linked ones, did not recover the three lineages, which we attribute to recent splitting. Analyses of the 13 introns combined revealed the same three groups as did the mtDNA and suggested that nuthatches experienced a trichotomous (or two indistinguishable) split(s) 1-2 million years ago (Mya) and have remained isolated with trifling if not zero gene flow since then, and the Asian group increased in population size. This result demonstrates the usefulness of mtDNA in discovering phylogeographic patterns. The use of multiple nuclear loci facilitated detection of an introgressed individual and improved estimates of process parameters such as divergence time and population expansion. We recommend that phylogeographic studies should be based on both mtDNA and nuclear genes.
... Phylogenetic and phylogeographic studies on North American birds have played a central role in understanding the impact of Pleistocene glacial-interglacial cycles on rates of speciation (Klicka and Zink, 1997;Johnson and Cicero, 2004;Zink et al., 2004). A number of phylogeographic studies on North American birds have found complex spatial and temporal patterns of diversification across multiple habitat types (e.g., montane highlands: Manthey et al., 2011;McCormack et al., 2011;van Els et al., 2012;Walstrom et al., 2012; mixed forest habitats: Klicka et al., 2011;scrub, edge, and non-forest habitats: Smith et al., 2011). The discordance in evolutionary histories observed in North America birds highlights the need to incorporate additional data from codistributed birds to better our understanding of how bird assemblages across the continent responded to Pleistocene glacial cycles. ...
... We used the program STRUCTURE (Pritchard et al. 2000) to determine the number of groups in the Common Sandpiper. We converted sequence data in two ways for the STRUCTURE analyses: (1) polymorphic sites for the five nuclear genes were formatted as single-nucleotide polymorphisms (SNP; Manthey et al. 2011;Walstrom et al. 2012;Hung et al. 2012); and (2) haplotypes for entire loci were used for each nuclear gene. Considering the uneven numbers of genes sequenced among individuals (Table 1) and inclusion of introns and exons, we used three datasets for the STRUCTURE analyses: (1) one dataset with all available nuclear data, (2) one dataset with individuals containing data for more than four nuclear genes, and (3) one dataset with all available intron data excluding data from the exon, Mc1r. ...
Article
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Although geographically structured mitochondrial DNA (mtDNA) trees often present straightforward evidence for independently evolving lineages, unstructured mtDNA trees are often interpreted as inconclusive or even misleading inferences of phylogeographic history. Some authors believe that stochastic coalescent processes or natural selection can result in mtDNA-based gene trees that fail to capture existing geographic structure. In this study, we sequenced four introns and one exon to test a published mtDNA tree that showed a lack of phylogeographic structure in the Common Sandpiper (Actitis hypoleucos). Neither individual nuclear gene trees nor analyses based on the five genes combined showed geographic structure in this widespread Palearctic wader. Multilocus neutrality tests suggested that the unstructured mtDNA tree was not biased by natural selection although the variation pattern at the exon, Mc1r, was not neutral. Coalescence-based analyses showed that this species experienced a recent population expansion, which could explain the lack of population structure. Overall, the mtDNA results were consistent with those based on nuclear loci in suggesting a lack of strong population structure and a recent population increase. However, multiple genes are needed to quantify demographic history such as timing and extent of effective population size change.
... 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. ...
Article
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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.
... 3.7 (Posada and Crandall 1998). We ran BEAST and * BEAST for 200 million generations, sampling every 2000 steps, using a Yule speciation tree prior, a UPGMA starting tree, a log normal relaxed uncorrelated molecular clock, and mutation rates of 2.9 ϫ 10 Ϫ8 substitutions/site/year for the ND2 , 1.67 ϫ 10 Ϫ9 substitutions/site/ year for the 20454, 1.2 ϫ 10 Ϫ9 substitutions/site/year for the GAPDH, and 1.7 ϫ 10 Ϫ9 substitutions/site/year for TGFB and MUSK, according to rates reported previously for those or similar genes in birds (Weir and Schluter 2008, Smith and Klicka 2010, Lerner et al. 2011, Lim and Sheldon 2011, Manthey et al. 2011, Sly et al. 2011. Because MUSK is a Z-linked gene (Kimball et al. 2009) their hemizygosis was considered in the analysis by setting the ploidy type as X while constructing the BEAUti (Drummond et al. 2012b) fi le. ...
Article
We used multilocus phylogeographic analyses, morphometric measurements, and environmental niche models (ENMs) to analyze the recent evolution of the golden vireo Vireo hypochryseus, a Mexican endemic species. Vireo hypochryseus is made up of two phylogeographically structured mitochondrial DNA clades that probably diverged 132 000 yr ago. One clade comprised individuals from mainland Sinaloa and the Tres Mar í as islands in the northwest, and the other included individuals from the remaining range of the species. Th is marked phylogeographic structure contrasts with the low genetic structure reported for temperate North American vireos. The nuclear DNA markers also showed some geographic differences in allele frequency, but did not exhibit a clearphylogeographic structure. The morphometric analyses suggested a decreasing north to south cline, with the largest individuals located in the Tres Marías islands. The ENMs did not support a scenario of geographic fragmentation of the environmental conditions of the area in which V. hypochryseus has inhabited over the last 130 000 yr. However, a model of isolation by resistance based on the actual configuration of climatic conditions in western Mexico did explain a major proportion of both the mitochondrial DNA distances and the differences in size, while a model of isolation by distance explain a low proportion of such differences. Therefore, the recent history of V. hypochryseus was likely shaped by historical habitat fragmentation due to fluctuating environmental conditions in the mainland that produced a phylogeographic print, and natural selection on morphological traits in the insular population, suggesting an active diversifi cation of endemic lineages in the Mexican dry forest.
... In brief, this program considers variation among loci simultaneously and attempts to determine whether there is more than one genetically distinct group represented in the sample. The seven variable nuclear loci were formatted as single-nucleotide polymorphisms (SNP; see Manthey et al. 2011). The STRUCTURE analyses assumed an admixture model, correlated allele frequencies, and a fixed lambda value (which was inferred by setting K = 1 and allowing lambda to be estimated in an initial analysis). ...
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An important step in conservation is to identify whether threatened populations are evolutionarily discrete and significant to the species. A prior mitochondrial DNA (mtDNA) phylogeographic study of the California Gnatcatcher (Polioptila californica) revealed no geographic structure and, thus, did not support the subspecies validity of the threatened coastal California Gnatcatcher (P. c. californica). The U.S. Fish and Wildlife Service concluded that mtDNA data alone were insufficient to test subspecies taxonomy. We sequenced eight nuclear loci to search for historically discrete groupings that might have been missed by the mtDNA study (which we confirmed with new ND2 sequences). Phylogenetic analyses of the nuclear loci revealed no historically significant groupings and a low level of divergence (G(ST) = 0.013). Sequence data suggested an older population increase in southern populations, consistent with niche modeling that suggested a northward range expansion following the Last Glacial Maximum (LGM). The signal of population increase was most evident in the mtDNA data, revealing the importance of including loci with short coalescence times. The threatened subspecies inhabits the distinctive Coastal Sage Scrub ecosystem, which might indicate ecological differentiation, but a test of niche divergence was insignificant. The best available genetic, morphological, and ecological data indicate a southward population displacement during the LGM followed by northward range expansion, without the occurrence of significant isolating barriers having led to the existence of evolutionarily discrete subspecies or distinct population segments that would qualify as listable units under the Endangered Species Act. Received 19 December 2012, accepted 19 April 2013.
... 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.
... We used the Bayesian method of individual genotype assignment in the program STRUC-TURE 2.3 (Pritchard et al. 2000) to test the hypothesis of no deep structure (K = 1) versus multiple clusters (K > 1). We coded our nuclear loci as SNPs (single nucleotide polymorphisms; following Manthey et al. 2011) to calculate K with values between 1 and 20 clusters using the admixture (ancient panmixia) and nonadmixture models (ancient fragmentation) with sampling locality as a prior and both correlated and uncorrelated allele frequencies (similar results therefore only correlated frequencies reported), 20 repetitions per cluster with 1 9 10 6 iterations and a burn-in of 100,000 steps to ensure reproducibility (Gilbert et al. 2012), and a fixed lambda value (which was inferred by setting K = 1 and allowing lambda to be estimated in an initial analysis). We used the DK method (Evanno et al. 2005) to identify the best estimate of K in STRUCTURE HARVESTER (Earl 2012). ...
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The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire-dependent communities. We studied an endangered juniper–oak shrubland specialist, the black-capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, preda-tion, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long-term history of the fire regime and ecological niche models representing the mid-Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present.
... In all population models, Texas individuals (groups D and E; Fig. 5) were an admixture of at least two genetic clusters, while Missouri and Oklahoma birds (groups A-C; Fig. 5) were characterized by one genetic background at all K values. California birds (groups I and H; Fig. 5) were clustered with specimens from Arizona, Mexico and Nevada for K = 2, but this genetic background was only partially shared at K values of 3 and 4. Thus, at these higher values of K, groups F and G show (Farrington et al. 2014;Hart et al. 2014;Manthey et al. 2011) is to perform separate analyses on different geographic regions. Thus, we further analyzed population structure by completing analyses for the eastern and western sub-clades with K = 1-4, and we found K = 2 and K = 3 received the best likelihood scores (Fig. 5). ...
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The Bell’s Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.
... In any case, high dispersal rates are facilitated by the lack of physical barriers, such as mountain ridges or areas of inhospitable habitat, which have been shown to result in genetic differentiation in other species (Manthey, Klicka, & Spellman, 2011 shows no major ecological discontinuities that would suggest differences in environmental selective pressures. Furthermore, Z. l. pugetensis readily accepts human-influenced habitats such as gardens, parks, and pastures, which promotes a relatively continuous distribution of this subspecies (Baptista, 1977;Chilton & Lein, 1996). ...
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Populations within a species can show geographic variation in behavioral traits that affect mating decisions or limit dispersal. This may lead to restricted gene flow, resulting in a correlation between behavioral variation and genetic differentiation. Populations of a songbird that differ in a learned behavioral trait, their song dialects, may also differ genetically. If song dialects function as mating barriers, evolutionary processes such as genetic drift should lead to divergence in allele frequencies among dialect populations. The Puget Sound white-crowned sparrow (Zonotrichia leucophrys pugetensis) is an excellent study system with a well-defined series of song dialects along the Pacific Northwest coast. A previous study found low genetic differentiation based on four microsatellite loci; however, available loci and analyses techniques have since dramatically improved and allow us to reassess gene flow in this species. We also add extra samples to fill in gaps and add a new level of analysis of geographic variation. Based on acoustic similarities, we group six song dialects into two geographically larger “northern” and “southern” song themes. One southern dialect is acoustically more similar to dialects in the north, which makes the genetic profile of birds singing this dialect particularly interesting. Traditional F-statistics, analysis of molecular variance as well as Bayesian techniques confirmed the earlier result that geographic variation in song does not correlate with the neutral genetic structure of the sampled dialect populations. The song themes also did not differ genetically, and the origin of the extralimital northern-theme dialect cannot be determined. We compare this result to findings in several other species and discuss how the timing of learning and dispersal allow vocalizations to vary independently of patterns of genetic divergence.
... Patterns observed here are not unusual in montane regions, where inhospitable lowlands can produce "sky island" archipelagos that isolate populations of habitat specialists that may be well-connected in other times or places (Brown, 1971;Lomolino et al., 1989;Manthey, Klicka, & Spellman, 2011;Phillipsen et al., 2015;Schoville, Stuckey, & Roderick, 2011). It is interesting that such patterns transfer to strong fliers like bumble bees, for which many species exhibit high gene flow and near-panmixia (Woodard et al., 2015). ...
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Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using Restriction‐site Associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius across latitude and altitude in mountain ranges from California, Oregon, and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, with B. vosnesenskii exhibiting relatively consistent levels of genetic diversity across its range, while B. bifarius has reduced genetic diversity at low latitudes, where it is restricted to high elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems. This article is protected by copyright. All rights reserved.
... For each matrix analyzed, we simulated 1 × 10 6 datasets and obtained summary statistics per scenario in each simulation. Based on rates reported previously for birds [141][142][143][144][145], we used an HKY mutation model with a uniform prior distribution, a mean mutation rate with a gamma distribution set to 2.0 × 10 − 8 substitutions/site/year (min = 1.6 × 10 − 8 , max = 2.9 × 10 − 8 substitutions/site/year) The posterior probabilities of competing scenarios were computed using a logistic regression on the 1% of simulated datasets closest to the observed data. The selected scenario was that with highest probability value and a non-overlapping 95% confidence interval. ...
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Background: Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results: We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions: Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.
... While divergences once linked to the Pleistocene glacial cycles appear to pre-date the Pleistocene (Zink & Slowinski 1995; although mutlilocus data sets may revise these figures in future), many divergences within currently recognized North American bird species are clearly linked to the glacial cycles [S. carolinensis (this study); Aphelocoma (McCormack et al. 2010); Poecile gambeli ; Certhia americana (Manthey et al. 2011b); Passerella iliaca (Zink 1994); Dendragapus obscurus (Barrowclough et al. 2004)], and multiple boreal sister taxa, both within and between species, have been found to have diverged during the Pleistocene (Weir & Schulter 2004), which is consistent with a hypothesis concerning the importance of the Pleistocene glacial cycles in the diversification of North American birds posed by Klicka & Zink (1997 ...
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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.
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Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re‐examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation‐with‐migration model suggests that the north–south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast‐specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P. nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 214–226.
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Contrasting multiple organisms with similar contemporary distributions, researchers can identify shared evolutionary patterns and provide historical context for community composition. We used three species complexes with overlapping distributions in Southeastern China and surrounding islands to explore the phylogeographic history of the region. Despite similar geographic distributions, genetic data revealed few congruent patterns, but all complexes displayed genetic divergence for Taiwanese populations. Additionally, niche modeling and divergence dating did not find support for diversification associated with the Last Glacial Maximum [Current Zoology 61 ( 5): 943-950, 2015].
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Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants, and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or Restriction site Associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted (‘capture’) resequencing emerge as the methods of choice for scaling up the sampling of populations, species, and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations. This article is protected by copyright. All rights reserved.
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The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of Tanzanian local chickens (Ching’wekwe, Kuchi, Morogoro-medium, Pemba and Unguja) from eight regions were studied. Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba and Unguja were grouped together, while Ching'wekwe stood out because of their disproportionate short shanks and ulna bones. Kuchi formed an independent group owing to their comparably long body sizes. Microsatellite analysis revealed three clusters of Tanzanian chicken populations. These clusters encompassed i) Morogoro-medium and Ching’wekwe from Eastern and Central Zones ii) Unguja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions, which formed an independent cluster. Sequence polymorphism of D-loop region was analysed to disclose the likely maternal origin of Tanzanian chickens. According to reference mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of different genealogical origin. From haplotype network analysis, Tanzanian chickens probably originated on the Indian subcontinent and in Southeast Asia. The majority of Kuchi chickens clustered in a single haplogroup, which was previously found in Shamo game birds sampled from Shikoku Island of Japan in the Kōchi Prefecture. Analysis of phenotypic and molecular data, as well as the linguistic similarity of the breed names, suggests a recent introduction of the Kuchi breed to Tanzania.
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Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessary to explain current patterns. We searched for concordant phylogeographic patterns and investigated their causes in three bird species (Momotus mexicanus, Melanerpes chrysogenys, and Passerina leclancherii) that belong to three different avian orders and are endemic to the northernmost range of the Neotropical dry forest. We obtained mitochondrial DNA (ND2 and COI or cyt b) and nuclear DNA (20454, GAPDH, MUSK, and TGFB) sequences for at least one locus from 162 individuals across all species and defined climatically stable areas using environmental niche model projections for the last 130,000 years to have a paleoenvironmental framework for the phylogeographic results. All three species showed marked phylogeographic structure, with breaks found in roughly similar areas, such as the border between the Mexican states of Guerrero and Oaxaca, and between southern Jalisco and Michoacán. Both of these regions are known biogeographic breaks among other taxa. Patterns of genetic diversity and differentiation were partially compatible with climatically stable areas. Coalescent analyses revealed recent population growth and estimated the deeper haplogroup divergence of all three taxa to have occurred within the last 600,000 years. The phylogeographic patterns found are noteworthy because they are maintained in a relatively small area for bird species with continuous ranges, and highlight a unique situation when compared to phylogeographic patterns found in other studies of Neotropical birds that have stressed the role of geographic barriers to explain intraspecific differentiation. Our results point to a scenario of population isolation resulting in the present phylogeographic structure, likely a result of historical climate fluctuations that have fragmented and reconnected the Neotropical dry forest. This study contributes to a growing body of evidence indicating active diversification of endemic lineages in the northern Neotropical dry forest region.
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Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era of increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit of these models to the data has rarely been tested. Here we develop a posterior predictive simulation-based model check for a commonly used multispecies coalescent model, implemented in *BEAST, and apply it to 25 published data sets. We show that poor model fit is detectable in the majority of data sets; that this poor fit can mislead phylogenetic estimation; and that in some cases it stems from processes of inherent interest to systematists. We suggest that as systematists scale up to phylogenomic data sets, which will be subject to a heterogeneous array of evolutionary processes, critically evaluating the fit of models to data is an analytical step that can no longer be ignored. [Gene duplication and extinction; gene tree; hybridization; model fit; multispecies coalescent; next-generation sequencing; posterior predictive simulation; species delimitation; species tree.]
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The study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns, and understand the statistical power of differentiating alternative diversification modes. We incorporate published datasets to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan deserts of North America, to synthesize phylogeographic structuring across the community with respect to organismal functional traits. We then use a simulation and machine learning pipeline to assess the power of phylogeographic model selection. Taxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses vary concordantly with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation-by-environment are the primary mechanisms purported to structure taxa. Simulations reveal that in spatially-explicit isolation-with-migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation-by-distance can confound the interpretation of evolutionary history and model selection by producing easily-confusable results. By synthesizing phylogeographic data for the Cochise Filter Barrier we show a pattern where barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying the modes of differentiation across the barriers for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.
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Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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The Speckled Rattlesnake (Crotalus mitchellii) is a polytypic taxon presently composed of five subspecies that range across southwestern North America, including the Baja Peninsula and islands in the Pacific Ocean and Sea of Cortes. The principles of genealogical concordance were employed to test the taxonomic status of three of the five subspecies (C. m. mitchellii, C. m. pyrrhus, and C. m. stephensi). We used two molecular marker systems: mitochondrial (mt) DNA ATPase 8 and 6 genes (675 base pairs, bp), and introns 5 and 6 of the nuclear (n) DNA ribosomal protein (RP) gene (449 bp). These markers were evaluated across 104 individuals of C. mitchellii: C. m. mitchellii (n = 3), C. m. pyrrhus (n = 83), C. m. stephensi (n = 18), with Sistrurus c. catenatus as the distant outgroup. Deep phylogenetic splits were detected in the subspecies of C. mitchellii, with 5.0-6.4% mtDNA sequence divergence (SD) separating C. m. mitchellii and C. m. pyrrhus, while C. m. mitchellii and C. m. stephensi had SD values of 6.4-7.3%. Similarly, C. m. pyrrhus and C. m. stephensi had SD values of 5.2-6.7%. In addition, C. m. mitchellii and C. m. pyrrhus were identical in all 449 intron bp, but C. m. stephensi differed from both at a single nucleotide polymorphism. Our molecular results diagnose C. m. stephensi as sister to mainland subspecies of the C. mitchellii complex, a result consistent with certain head scalation characters and its northernmost geographic distribution in this complex. Furthermore, four morphological synapomorphies (supraocular scales prominently ridged and/or creased, contact between rostral and prenasal scales, ground coloration of tail congruent with that of body, and black rings in the distal 15% of the tail) also diagnose C. m. stephensi from all other subspecies of C. mitchellii. We hypothesize that the northern distribution of C. m. stephensi likely resulted from two vicariant events: Pliocene expansion of the Sea of Cortes as the Salton Trough, and Pliocene development of the lacustrine Bouse Embayment along the Colorado River drainage. Despite earlier conclusions based on morphology, our molecular results showed no evidenc eo f intergradation between C. m. pyrrhus and C. m. stephensi. Based on the principles of genealogical concordance, we advocate that C. m. stephensi be elevated to a full species, which renders a minimum of two species within the C. mitchellii clades we examined.
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Separated throughout most of the Cenozoic era, North and South America were joined during the mid-Pliocene when the uplift of Panama formed a land bridge between these two continents. The fossil record indicates that this connection allowed an unprecedented degree of inter-continental exchange to occur between unique, previously isolated biotic assemblages, a phenomenon now recognized as the “Great American Biotic Interchange”. However, a relatively poor avian fossil record has prevented our understanding the role of the land bridge in shaping New World avian communities. To address the question of avian participation in the GABI, we compiled 64 avian phylogenetic studies and applied a relaxed molecular clock to estimate the timing of trans-isthmus diversification events. Here, we show that a significant pulse of avian interchange occurred in concert with the isthmus uplift. The avian exchange was temporally consistent with the well understood mammalian interchange, despite the presumed greater vagility of birds. Birds inhabiting a variety of habitats and elevational zones responded to the newly available corridor. Within the tropics, exchange was equal in both directions although between extratropical and tropical regions it was not. Avian lineages with Nearctic origins have repeatedly invaded the tropics and radiated throughout South America; whereas, lineages with South American tropical origins remain largely restricted to the confines of the Neotropical region. This previously unrecognized pattern of asymmetric niche conservatism may represent an important and underappreciated contributor to the latitude diversity gradient.
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The growing use of molecular systematics in conservation has increased the importance of accurate resolution of taxonomic units and relationships. DNA data relate most directly to genealogies, which need not have perfect relationships with species limits and phylogenies. We used a multilocus gene tree approach to elucidate the relationships between four endangered Central American iguanas. We found support for the proposition that the described species taxa correspond to distinct evolutionary lineages warranting individual protection. We combined gene trees to estimate a phylogeny using Bayesian Estimation of Species Trees (BEST), minimizing deep coalescence, Species Trees from Average Ranks (STAR), and traditional concatenation. The estimate from concatenation conflicted with the other methods, likely owing to the disproportionate effect of mtDNA on concatenated analyses. This illustrates the importance of appropriate treatment of multilocus sequence data in phylogenetics. Our results indicate that these species have gone through recent and rapid speciation, resulting in four closely related narrow-range endemics. Keywords Ctenosaura -BEST-Minimizing deep coalescence-Estimating species trees-Species designation-Gene trees
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Martínez spruce (Picea martínezii T.F. Patterson) is a conifer currently passing through a bottleneck, reduced to a few relict populations totaling less than 800 trees. We used isozyme markers to analyze the mating system and survey the level of genic diversity in two populations. The mating system was characterized by a high frequency of selfing. The multilocus outcrossing rates (tm) and 95% confidence intervals were only 0.399 (0.197 < tm < 0.601) for the smallest population and 0.589 (0.475 < tm < 0.703) or 0.685 (0.465 < tm < 0.905), depending on year, for the largest. These are among the lowest rates of outcrossing observed in conifers. The fixation indices for the two populations were –0.058 and 0.121, less than expected for such high levels of selfing. Expected heterozygosity, unbiased He, based on 22 loci in 13 enzyme systems, was 0.121 and 0.101 in the two populations. The proportion of the total genic diversity between populations, FST, was 2.4%. Nm, the number of migrants per generation, was about 1.00 or 10.17, depending on the method of estimation. The time since the two populations were isolated was estimated from Nei’s genetic distance as only 150 to 15 000 years, which is consistent with a hypothesis of population collapse during late Pleistocene or Holocene warming. We discuss the implications for conservation
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Author Summary In DNA, information is encoded as a sequence of four types of building blocks–nucleotides. The most common technique for determining such sequences, the Sanger method, outputs a single consensus for a pool of DNA molecules in the analyzed sample. When these are identical, each site in the output contains a single nucleotide call. Yet, samples from organisms with two sets of chromosomes generally contain two types of DNA molecules (alleles), each derived from one parent. If, due to insertion or deletion (indel) mutations, one allele contains extra nucleotides, most sites in the sequencing output beyond the mutation site will contain pairs of nucleotide calls. While signaling the presence of a potentially important mutation, such output cannot be read directly and often gets discarded. Here we describe an algorithmic method which accurately reconstructs the pair of allelic sequences from the observed complex pattern of calls. Unlike most existing computational approaches to the problem, our method does not require knowledge of one of the involved sequences to use as a reference, nor any other additional information. Therefore, it can facilitate sequencing of indel-rich regions of genomes and speed up discovery and characterization of indel mutations, including those causing diseases in humans.
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Pine and oak woodlands are common North American floral communities with distinct regional species composition. The white-breasted nuthatch (Aves: Sitta carolinensis) is a common resident bird of North American pine and oak woodlands, and is distributed continentally across the highly disjunct distribution of these woodlands. We propose three historical hypotheses to explain the evolution of the white-breasted nuthatch in its principal habitat. (i) The species evolved in situ in the regional pine-oak communities and the isolation of populations in these regions is captured in cryptic genetic variation. (ii) Migration of individuals between regions is frequent enough to maintain the widespread distributions and prevent regional divergence. (iii) The species have recently expanded to occupy their current distributions and an insufficient amount of time has passed for divergence to occur. Phylogenetic analysis of mitochondrial DNA (ND2 gene) variation (N = 216) in the white-breasted nuthatch reveals four reciprocally monophyletic clades concordant with the distribution of the regional North American pine and oak woodlands, and supports hypothesis 1 of in situ evolution of populations in the regional pine and oak communities. Within-clade population structure and demographic history are also discussed.
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Peripatric speciation and the importance of founder effects have long been controversial, and multilocus sequence data and coalescent methods now allow hypotheses of peripatric speciation to be tested in a rigorous manner. Using a multilocus phylogeographical data set for two species of salamanders (genus Hydromantes) from the Sierra Nevada of California, hypotheses of recent divergence by peripatric speciation and older, allopatric divergence were tested. Phylogeographical analysis revealed two divergent lineages within Hydromantes platycephalus, which were estimated to have diverged in the Pliocene. By contrast, a low-elevation species, Hydromantes brunus, diverged from within the northern lineage of H. platycephalus much more recently (mid-Pleistocene), during a time of major climatic change in the Sierra Nevada. Multilocus species tree estimation and coalescent estimates of divergence time, migration rate, and growth rate reject a scenario of ancient speciation of H. brunus with subsequent gene flow and introgression from H. platycephalus, instead supporting a more recent divergence with population expansion. Although the small, peripheral distribution of H. brunus suggests the possibility of peripatric speciation, the estimated founding population size of the species was too large to have allowed founder effects to be important in its divergence. These results provide evidence for both recent speciation, most likely tied to the climatic changes of the Pleistocene, and older lineage divergence, possibly due to geological events, and add to evidence that Pleistocene glacial cycles were an important driver of diversification in the Sierra Nevada.
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RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP3 also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. The new RDP3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC. Availability: RDP3 is available for free from its web site http://darwin.uvigo.es/rdp/rdp.html Contact: darrenpatrickmartin@gmail.com Supplementary information: The RDP3 program manual contains detailed descriptions of the various methods it implements and a step-by-step guide describing how best to use these.
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I investigated the impacts of phylogeographic sampling decisions on species tree estimation in the Sceloporus undulatus species group, a recent radiation of small, insectivorous lizards connected by parapatric and peripatric distribution across North America, using a variety of species tree inference methods (Bayesian estimation of species trees, Bayesian untangling of concordance knots, and minimize deep coalescences). Phylogenetic analyses of 16 specimens representing 4 putative species within S. "undulatus" using complete (8 loci, >5.5 kb) and incomplete (29 loci, >23.6 kb) nuclear data sets result in species trees that share features with the mitochondrial DNA (mtDNA) genealogy at the phylogeographic level but provide new insights into the evolutionary history of the species group. The concatenated nuclear data and mtDNA data both recover 4 major clades connecting populations across North America; however, instances of discordance are localized at the contact zones between adjacent phylogeographic groups. A random sub-sampling experiment designed to vary the phylogeographic samples included across hundreds of replicate species tree inferences suggests that inaccurate species assignments can result in inferred phylogenetic relationships that are dependent upon which particular populations are used as exemplars to represent species and can lead to increased estimates of effective population size. For the phylogeographic data presented here, reassigning specimens with introgressed mtDNA genomes to their prospective species, or excluding them from the analysis altogether, produces species tree topologies that are distinctly different from analyses that utilize mtDNA-based species assignments. Evolutionary biologists working at the interface of phylogeography and phylogenetics are likely to encounter multiple processes influencing gene trees congruence, which increases the relevance of estimating species trees with multilocus nuclear data and models that accommodate deep coalescence.
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Background: Speciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of species: the independent evolution of a population-level lineage. The comprehensive delimitation of species within biodiversity hotspots, regardless of their level of divergence, is important for understanding the factors that drive the diversification of biota and for identifying them as targets for conservation. However, delimiting recently diverged species is challenging due to insufficient time for the differential evolution of characters--including morphological differences, reproductive isolation, and gene tree monophyly--that are typically used as evidence for separately evolving lineages. Methodology: In this study, we assembled multiple lines of evidence from the analysis of mtDNA and nDNA sequence data for the delimitation of a high diversity of cryptically diverged population-level mouse lemur lineages across the island of Madagascar. Our study uses a multi-faceted approach that applies phylogenetic, population genetic, and genealogical analysis for recognizing lineage diversity and presents the most thoroughly sampled species delimitation of mouse lemur ever performed. Conclusions: The resolution of a large number of geographically defined clades in the mtDNA gene tree provides strong initial evidence for recognizing a high diversity of population-level lineages in mouse lemurs. We find additional support for lineage recognition in the striking concordance between mtDNA clades and patterns of nuclear population structure. Lineages identified using these two sources of evidence also exhibit patterns of population divergence according to genealogical exclusivity estimates. Mouse lemur lineage diversity is reflected in both a geographically fine-scaled pattern of population divergence within established and geographically widespread taxa, as well as newly resolved patterns of micro-endemism revealed through expanded field sampling into previously poorly and well-sampled regions.
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Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and extinction. Lineage sorting could also be called deep coalescence , the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relationships. Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the probability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of inter-breeding.
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Unlabelled: BEST implements a Bayesian hierarchical model to jointly estimate gene trees and the species tree from multilocus sequences. It provides a new option for estimating species phylogenies within the popular Bayesian phylogenetic program MrBayes. The technique of simulated annealing is adopted along with Metropolis coupling as performed in MrBayes to improve the convergence rate of the Markov Chain Monte Carlo algorithm. Availability: http://www.stat.osu.edu/~dkp/BEST.
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A genealogical relationship among genes at a locus (gene tree) sampled from three related populations was examined with special reference to population relatedness (population tree). A phylogenetically informative event in a gene tree constructed from nucleotide differences consists of interspecific coalescences of genes in each of which two genes sampled from different populations are descended from a common ancestor. The consistency probability between gene and population trees in which they are topologically identical was formulated in terms of interspecific coalescences. It was found that the consistency probability thus derived substantially increases as the sample size of genes increases, unless the divergence time of populations is very long compared to population sizes. Hence, there are cases where large samples at a locus are very useful in inferring a population tree.
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This book is a unique and integrated account of the history of North American vegetation and paleoenvironments over the past 70 million years. It includes discussions of the modern plant communities, causal factors for environmental change, biotic response, and methodologies. The history reveals a North American vegetation that is vast, immensely complex, and dynamic.
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We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure. distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct, available at http://www.cmb.usc.edu/~noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
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The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories. • coalescent theory • importance sampling • molecular clock • yeast
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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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Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation in these jays coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's rule could account for some differences in timing estimates between mitochondrial DNA and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
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Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.
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Bryan Carstens is interested in methodological approaches to phylogenetics and phylogeography, particularly in how the approaches that are adopted while analyzing phylogeographic data can influence our confidence in the results. Noah Reid is interested in phylogentic theory and comparative phylogeography of neotropical insects. Holly Stoute conducted this research while supported as a summer researcher by the HHMI; she is interested in evolutionary genetics and developmental biology, and hopes to enter a Ph.D. program in the Fall of 2010.
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Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a "species tree" (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.
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Newts of the genus Triturus are parapatrically distributed across Europe. Within this group, the crested newts (Triturus cristatus superspecies) radiated in a short temporal interval. Given the relatively short timespan in between branching events and to address the gene tree-species tree problem, we sequenced two mitochondrial and five nuclear genes from populations representing the distribution range of all the five crested newt species. We built gene trees using non-hierarchical Bayesian phylogenetics and phylogenetic networks, and a species tree with a recently developed method, which uses a hierarchical Bayesian approach. While the single gene trees did not provide resolution, the hierarchical Bayesian method yielded an almost fully resolved species tree, even though branching events followed one another closely. Results show a previously undetected basal dichotomy between T. karelinii and the other four species and a deep differentiation of T. karelinii in two lineages, here raised to full species status.
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The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.
Article
Multilocus analysis of phylogeography and population history is a powerful tool for understanding the origin, dispersal, and geographic structure of species over time and space. Using 36 genetic markers (29 newly developed anonymous nuclear loci, six introns and one from mitochondrial DNA, amounting to over 15 kb per individual), we studied population structure and demographic history of the red-backed fairy wren Malurus melanocephalus, a small passerine distributed in the northern and eastern part of Australia across the Carpentarian barrier. Analysis of anonymous loci markers revealed large amounts of genetic diversity (pi= 0.016 +/- 0.01; average number of SNPs per locus = 48; total number of SNPs = 1395), and neither nuclear nor mitochondrial gene trees showed evidence of reciprocal monophyly among Cape York (CY), Eastern Forest (EF), and Top End (TE) populations. Despite traditional taxonomy linking TE and CY populations to the exclusion of EF, we found that the CY population is genetically closer to the EF population, consistent with predicted area cladograms in this region. Multilocus coalescent analysis suggests that the CY population was separated from the other two regions approximately 0.27 million years ago, and that significant gene flow between the ER and the CY populations ( approximately 2 migrants per generation) suggests geographic continuity in eastern Australia. By contrast, gene flow between the CY and the TE populations has been dampened by divergence across the Carpentarian barrier.
Article
We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.
Article
The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
Article
There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.
Article
The main purpose of this article is to present several new statistical tests of neutrality of mutations against a class of alternative models, under which DNA polymorphisms tend to exhibit excesses of rare alleles or young mutations. Another purpose is to study the powers of existing and newly developed tests and to examine the detailed pattern of polymorphisms under population growth, genetic hitchhiking and background selection. It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations. Background selection gives rise to quite different polymorphic patterns than does logistic population growth or genetic hitchhiking, although all of them show excesses of rare alleles or young mutations. We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed.
Article
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
Article
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 (theta) to T and the effect of uncertainty in theta on estimates of population divergence (tau) 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 tau decrease when the range over which ancestral population size theta is assumed to be distributed decreases and when tau increases; they generally exclude zero when tau/(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding tau = 0 is roughly that l tau/(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
Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.