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Accounting for coalescent stochasticity in testing phylogeographical hypotheses: Modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus
Abstract
Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so in the context of explicit hypothesis testing. Here, we provide an example from the Idaho giant salamander (Dicamptodon aterrimus) using 118 mtDNA sequences, nearly 2 kb in length. This species is endemic to mesic forests in northern and central Idaho, and several a priori hypotheses have been erected based both on palaeoclimatic grounds and from phylogeographical studies of codistributed amphibians. Phylogenetic analysis of the D. aterrimus data suggests an expansion from a single refugium south of the Salmon River, whereas the inference from nested clade analysis is one of expansion from a single refugium in the Clearwater drainage. Explicit testing of these hypotheses, using geographically structured coalescent simulations to erect null distributions, indicates we can reject expansion from the Clearwater drainage (pCLW = 0.089), but not expansion from the South Fork of the Salmon drainage (pSAL = 0.329). Furthermore, data from codistributed amphibians suggest that there may have been two refugia, and an amova shows that most of the molecular variance partitioned between the Clearwater and the Salmon drainages (54.40%; P < 0.001) and within drainages (43.61%; P < 0.001). As a result, we also tested three a priori hypotheses which predicted that both the Clearwater and Salmon drainages functioned as refugia during the late Pleistocene; we could reject (PCORD = 0.019) divergence dates during the Cordilleran glacial maxima [c. 20 000 years before present (ybp)], during the Sangamon interglacial (c. 35 000 ybp; pSANG = 0.032), as well as pre-Pleistocene divergence (c. 1.7 Ma; ppP < 0.001). Mismatch distributions and Tajima's D within the individual drainages provide further support to recent population expansion. This work demonstrates coalescent stochasticity is an important phenomenon to consider in testing phylogeographical hypotheses, and suggests that analytical methods which fail to sufficiently quantify this uncertainty can lead to false confidence in the conclusions drawn from these methods.
... Aunque la fi logeografía se ha utilizado para conocer los patrones históricos de poblaciones que pertenecen a la misma especie, los estudios en ésta área también pueden ser utilizados para inferir procesos demográfi cos históricos, como fl ujo génico, tamaño efectivo de la población, cuellos de botella y secuencias de colonización (Templeton, 1998;Irwin, 2002;Carstens et al., 2005, Rissler y Apodaca, 2007. Además, los estudios fi logeográfi cos son cada vez más utilizados en la delimitación de especies y en el reconocimiento de unidades más precisas de conservación (Avise et al., 1987;Moritz y Faith, 1998;Avise, 2000;Wiens y Penkrot, 2002;). ...
... El surgimiento de la fi logeografía no hubiera sido posible sin el avance de dos aspectos de la biología evolutiva. Por un lado, el aspecto conceptual, que impulsó la aplicación de la teoría de la coalescencia al estudio de procesos microevolutivos; y por el otro, el tecnológico, que permitió disponer de datos sobre la variabilidad intraespecífi ca en forma de secuencias de DNA (Lanteri y Confalonieri, 2003;Carstens et al., 2005;Beheregaray et al., 2008;Avise, 2009;Hickerson et al., 2010). ...
... Los tiempos de coalescencia pueden ser infl uenciados por diversos procesos que ocurren a nivel poblacional, tales como fl uctuaciones en el tamaño de las poblaciones, existencia de selección natural o variaciones en el fl ujo génico (Harding, 1996;Lanteri y Confalonieri, 2003;Vázquez-Domínguez et al., 2009). Por ejemplo, una población que ha tenido un crecimiento exponencial reciente coalescerá más rápidamente que una población que ha estado en una estasis demográfi ca o que ha disminuido de tamaño (Cuenca et al., 2003;Carstens et al., 2005;DeChaine y Martin, 2006;Hickerson et al., 2010). Los linajes individuales pueden rastrearse en el tiempo (t 1 , t 2 & t 3 ) para identificar diferentes eventos coalescentes. ...
... The paleodistributional models are then used as a framework for statistical phylogeographic hypothesis testing, in which parametric simulation is used to construct null distributions of the expected variance of relevant parameters under competing historical scenarios (e.g., Knowles 2004). This approach has proven to be a useful tool for phylogeographic research (e.g., Knowles 2001;Carstens et al. 2005a;DeChaine and Martin 2005;Russell et al. 2005;Steele and Storfer 2006), but in the absence of explicit reconstructions of the past range of the focal organism. By integrating paleodistributional models and statistical phylogeography, we hope to increase the realism of historical models, thereby improving phylogeographic inferences about the relative importance of particular climatic events to the formation of population genetic structure. ...
... Phylogeographic hypotheses were tested previously in Dicamptodon spp. (Carstens et al. 2005a;Steele and Storfer 2006) and were not repeated here. Sequence data with sufficient variability for testing these phylogeographic hypotheses are not currently available in the other species (e.g., Thu. ...
... plicata, paleodistributional models (see online Supplementary Figure S1b, c) suggest that two disjunct regions contained the most suitable habitat, one in the Cascades and one in the northern Rocky Mountains. For these lineages, the models of past habitat suitability are largely congruent with the inference that populations persisted throughout the Pleistocene in multiple glacial refugia (Brunsfeld and Sullivan 2005), with only D. aterrimus apparently confined to a single refugium (see Carstens et al. 2005a). Models of two refugia cannot be rejected in A. montanus and P. idahoensis, and genetic data for these species as well as the codistributed plant Cardamine constancei (Brunsfeld and Sullivan 2005) suggest structured refugia. ...
... The second hypothesis (dual refugia hypothesis) is suggested by recent phylogeographic studies of Plethodon vandykei (Carstens et al., 2004a) and Dicamptodon aterrimus (Carstens et al., 2004b), which indicate that the Clearwater River and South Fork Salmon River valleys, respectively, served as refugia for these species during Pleistocene glaciation. These salamander species have ecological tolerances similar to that of the tailed frog; therefore, we propose that both refugia were used by A. montanus. ...
... The second hypothesis (dual refugia hypothesis) is suggested by recent phylogeographic studies of Plethodon vandykei (Carstens et al., 2004a) and Dicamptodon aterrimus (Carstens et al., 2004b), which indicate that the Clearwater River and South Fork Salmon River valleys, respectively, served as refugia for these species during Pleistocene glaciation. These salamander species have ecological tolerances similar to that of the tailed frog; therefore, we propose that both refugia were used by A. montanus. ...
... 62,No. 3 Clearwater drainage at the close of the Pleistocene (Carstens et al., 2004a). Similar analysis of sequences from the Idaho giant salamander (Dicamptodon atterimus) indicates expansion from the South Fork of the Salmon River (Carstens et al., 2004b). ...
In this paper we support the division of the previously monotypic genus Ascaphus into two species based on an analysis of 23 allozyme loci from 34 populations. We use maximum likelihood to estimate the Ascaphus phylogeny from the allozyme data and find strongly supported monophyletic Rocky Mountain and Pacific clades. In a nonhierarchal, model-based cluster analysis of the data, each of the 1085 individual genotypes is correctly assigned to either Ascaphus montanus or A. truei with a high probability. We also find a virtually fixed difference between the species at the Pgm-2 locus. Within A. truei, we find a lack of significant pairwise F-ST values among populations from the Coast and central Cascades Mountains, suggesting relatively recent range expansion or contemporary gene flow among these populations. Olympic Mountains populations form a discrete clade in the allozyme topology and are fixed for a unique allele at the Lap locus. These populations remain isolated from the remainder of the species' range based on pairwise FST values. The four southernmost A. truei populations each show significant allelic divergence from the remaining populations (based on pairwise F-ST values), suggesting climate-induced isolation. In addition, we extend mtDNA sampling within the Rocky Mountains and sequence 530 nucleotides from the mtDNA Cytochrome b (cyt b) gene in 12 previously unsampled A. montanus populations. This additional sampling defines the geographic extent of a southern mtDNA clade distinguished on average by 0.024 substitutions per site from the northern clade. We use nested clade analysis, a coalescent-based divergence by isolation with migration model (MDIV), maximum-likelihood estimation of the mtDNA topology, and Bayesian model-based genotype assignment, to test predictions from two hypotheses: the western refugia hypothesis, which claims that A. montanus persisted in refugia west of the Snake River during Pleistocene glacial maxima, and the dual refugia hypothesis, which asserts that A. montanus occupied refugia within the Salmon and Clearwater River Valleys during glacial maxima. Our data do not support predictions of the western refugia hypothesis. Nested-clade analysis, estimated dates of lineage divergence supplied by MDIV, and the mtDNA topology support predictions of the dual refugia hypothesis; however, the allozyme topology fails to support some of these predictions. Allozyme and mtDNA data endorse the preliminary recognition of a minimum of two Evolutionarily Significant Units (ESUs) within A. truei: (1) populations from the Olympic Mountains and (2) populations south of the Umpqua River. Two ESUs are also suggested within A. montanus: (1) populations south of the South Fork of the Salmon River, and (2) populations to the north and west of the Salmon River (including the Blue, Wallowa and Seven Devils Mountains). The MDIV analysis indicates an exchange rate of 10 migrants per generation between the northern ESU and the southern ESU.
... Genetic data from Hemphillia slugs (Rankin et al., 2019), Rocky Mountain tailed frog [Ascaphus montanus (Nielson et al., 2001;Metzger et al., 2015)] and Constance's bittercress [Cardamine constancei (Brunsfeld & Sullivan, 2005)] are all consistent with expansion from multiple refugia; however, there are other species that exhibit evidence of expansion from a single refugium [e.g. Idaho giant salamanders, Dicamptodon aterrimus (Carstens et al., 2005)]. ...
... That is, the river canyons of the Clearwater basin are some of the northernmost canyons that were free of glacial ice and probably served as a refugium for many extant species with high moisture-heat requirements. This moist-canyon ecosystem contains many plants and animals endemic to the NRMs, as well as regional endemics whose distributions are closely tied to the Clearwater drainage such as the bank monkeyflower [Mimulus clivicola (Lorain, 1992)], several species of byrrhid beetles (Johnson, 1987) and the snail Allogona lombardi (Burke, 2013). It is also interesting to note that a widespread species like A. k. occidentalis contains a distinct (all private haplotypes) Clearwater clade with relatively high diversity, suggesting this is a long-established population as well. ...
The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails Anguispira kochi occidentalis and Anguispira nimapuna. These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of A. k. occidentalis and A. nimapuna, we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of A. k. occidentalis and A. nimapuna. We then reconstruct the demographic history of A. k. occidentalis and A. nimapuna by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both A. k. occidentalis and A. nimapuna represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of A. k. occidentalis has been shaped by both historical isolation in refugia and more recent northward shifts, whereas A. nimapuna is represented by two populations with shallow divergence in an area of long-term habitat stability.
... For instance, winter conditions in some areas of interior Beringia during the last glacial maximum may have been warmer than those of interior Alaska during the present (Elias et al. 1997), while other areas experienced polar desert conditions. Substantial variability could also be explained by inherent genetic stochasticity and the attendant effects of highly variable demographic histories (Carstens et al. 2005;Hickerson et al. 2006b). By controlling for stochasticity, this comparative analysis provides evidence for multiple divergence events among the taxon pairs (at least 5 separate divergence events) within a Pleistocene timeframe, and for multiple different demographic responses. ...
... The coalescent-based approach to testing for simultaneous divergence that we implemented relies on a number of important assumptions that warrant further consideration (Carstens et al. 2005;DeChaine and Martin 2006;Hickerson et al. 2006b). ...
... Hudson 2002). The modelled population histories are often generated based on inferences obtained from geological data (Carstens et al. 2005), paleoclimatic data (Spellman & Klicka 2006), or based on previous genetic studies (Tsai & Carstens 2013), and the parameterizations used in the models can be derived from estimates from empirical data (Carstens et al. 2005). The parameter estimates based on the empirical data are then compared to the distribution of simulated values, allowing for the support or rejection of each hypothesis. ...
... Hudson 2002). The modelled population histories are often generated based on inferences obtained from geological data (Carstens et al. 2005), paleoclimatic data (Spellman & Klicka 2006), or based on previous genetic studies (Tsai & Carstens 2013), and the parameterizations used in the models can be derived from estimates from empirical data (Carstens et al. 2005). The parameter estimates based on the empirical data are then compared to the distribution of simulated values, allowing for the support or rejection of each hypothesis. ...
Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
... DNA was extracted from 10-20 mg tail clips, which had been stored in 90% EtOH, either with the DNeasy Tissue kit (Qiagen, Inc.; Valencia, CA), following manufacturer's instructions for rodent tails or using a standard phenol/chloroform extraction protocol . To amplify the Cytochrome b gene (Cyt b), we used the following primers from Carstens et al. (2005): tRNA-Threonine (5'-TTCAGCTTACAAGGCTGATGTTTT-3'); tRNA-Glucine (5'-TTGTATTCAACTATAAAAAC-3'); forward internal 5'-TCCACCCATACTTTTCTTATAAAGA-3'; reverse internal 5'-TAATTAGTGGATTTGCTGGTGTAA-3'). Amplicons were purified using polyethylene glycol precipitation, and sequencing reactions were performed with the BigDye Kit version 2.0 (Applied Biosystems, Inc.; Foster City, CA) with 20-40 ng of PCR product in 15 µl volumes. ...
... The basic premise of Nussbaum's hypothesis may be correct but would require that populations in the northern Cascades, from which the ancestors of D. copei diverged, were unable to escape advancing glaciers and that modern populations of D. tenebrosus have recently expanded into the north Cascades. Testing this hypothesis will require additional D. tenebrosus sampling, explicit phylogeographic modeling and coalescent-based hypothesis testing following Knowles (2001) and Carstens et al. (2005). Support for the sister-group relationship between D. tenebrosus and D. ensatus is high in our analyses, as indicated by MP (72) and ML (67) bootstrapping and Bayesian posterior probability (p = 0.9483). ...
... Phylogeographical methodologies typically do not undercut a phylogenetic hypothesis with well-resolved clades that correspond to geographically delimited populations, especially when comparative analyses are undertaken (Brunsfeld et al. 2001;Carstens et al. 2005). Populations that form well-supported reciprocally monophyletic lineages in phylogenetic analyses are useful to researchers conducting phylogeographical investigations, as the evolutionary history of the species can be inferred from the single phylogenetic hypothesis (Brunsfeld et al. 2001;Nielson et al. 2001;Demboski & Sullivan 2003;Carstens et al. 2005). ...
... Phylogeographical methodologies typically do not undercut a phylogenetic hypothesis with well-resolved clades that correspond to geographically delimited populations, especially when comparative analyses are undertaken (Brunsfeld et al. 2001;Carstens et al. 2005). Populations that form well-supported reciprocally monophyletic lineages in phylogenetic analyses are useful to researchers conducting phylogeographical investigations, as the evolutionary history of the species can be inferred from the single phylogenetic hypothesis (Brunsfeld et al. 2001;Nielson et al. 2001;Demboski & Sullivan 2003;Carstens et al. 2005). However, we must begin to question these methods if we are to understand the forces that influence the divergence process. ...
We fit a molecular data set, consisting of the rpL16 cpDNA marker and eight microsatellite loci, to the isolation-with-migration model as implemented in IMA to test a well-supported phylogenetic hypothesis of relationships within the Carex macrocephala species complex (Cyperaceae). The phylogenetic hypothesis suggests C. macrocephala from North America is reciprocally monophyletic and is sister to a reciprocally monophyletic clade of C. kobomugi. The North American C. macrocephala and C. kobomugi clade form a sister clade with a lineage of Asian C. macrocephala, thereby forming a paraphyletic C. macrocephala species. Not only does the phylogenetic hypothesis suggest C. macrocephala is paraphyletic, but it also suggests that the two lineages which share a partially overlapping distribution, Asian C. macrocephala and C. kobomugi, are not the most closely related. To test these relationships, we used coalescent-based population genetic models to infer divergence time for each lineage pair within the species complex. The coalescent-based models account for the stochastic forces which drive population divergence, and can account for the lineage sorting that occurs prior to lineage divergence. A drawback to phylogenetic-based phylogeographical analyses is that they do not account for stochastic lineage sorting that occurs between gene divergence and lineage divergence. By comparing the relative divergence time of the three main lineages within this group, Asian C. macrocephala, North American C. macrocephala, and C. kobomugi, we concluded that the phylogenetic hypothesis is incorrect, and the divergence between these lineages occurred during the Late Pleistocene epoch.
... Glacial phases during the Pleistocene had major effects on the distribution and demography of species globally (Hewitt 2000). Consequently, there have been many phylogeographic studies devoted to assessing the role of Pleistocene glacial phases in the history of species and formation of extant patterns of biodiversity (Avise 2000;Hewitt 2001Hewitt , 2004Knowles 2001;Carstens et al. 2005). Although ice sheets during glacial phases restricted biota to refugia in many regions, especially in the northern hemisphere, aridity and new land connections associated with lowered sea levels were the major earth history events that affected Australasia during Pleistocene glaciations (Hewitt 2000;Voris 2000). ...
... Although the discordance commonly observed between individual gene trees and population trees argues for caution when making historical inferences in biogeography, the statistical methodology applied here provides a simple probabilistic method for assessing hypothesised scenarios of population history (Knowles and Maddison 2002;Carstens et al. 2005). We can confidently reject both widespread genetic exchange among G. aprion populations during the LGM and prePleistocene hypotheses (e.g. ...
Glacial cycles during the Pleistocene reduced sea levels and created new land connections in northern Australia, where many currently isolated rivers also became connected via an extensive paleo-lake system, ‘Lake Carpentaria’. However, the most recent period during which populations of freshwater species were connected by gene flow across Lake Carpentaria is debated: various ‘Lake Carpentaria hypotheses’ have been proposed. Here, we used a statistical phylogeographic approach to assess the timing of past population connectivity across the Carpentaria region in the obligate freshwater fish, Glossamia aprion. Results for this species indicate that the most recent period of genetic exchange across the Carpentaria region coincided with the mid- to late Pleistocene, a result shown previously for other freshwater and diadromous species. Based on these findings and published studies for various freshwater, diadromous and marine species, we propose a set of ‘Lake Carpentaria’ hypotheses to explain past population connectivity in aquatic species: (1) strictly freshwater species had widespread gene flow in the mid- to late Pleistocene before the last glacial maximum; (2) marine species were subdivided into eastern and western populations by land during Pleistocene glacial phases; and (3) past connectivity in diadromous species reflects the relative strength of their marine affinity.
... The coalescent-based tests for simultaneous divergence that we implemented rely on a number of important assumptions that warrant further consideration (Carstens et al., 2005;De-Chaine & Martin, 2006;Hickerson et al., 2006a). Although variance around coalescent parameter estimates based on a single mitochondrial locus are broad and increasing the number of loci can improve divergence estimates (Hickerson et al., 2006b;Huang et al., 2011), inferences from msBayes have been shown to be robust to both single-locus data sets and small sample sizes (Hickerson et al., 2006a). ...
... We have tested a suite of eight pairs of small mammal taxa for simultaneous divergence across Beringia and rejected that hypothesis in favour of multiple distinct divergence events through time among these taxa. This explicit analysis of pairs of taxa extends the implications of multiple independent studies, while controlling for the genealogical stochasticity inherent in coalescent processes (Carstens et al., 2005;Hickerson et al., 2006a). Climate-driven changes have resulted in multiple diversification events among small mammals within Beringia, particularly during the late Quaternary. ...
Aim
Quaternary climate cycles played an important role in promoting diversification across the N orthern H emisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of H olarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.
Location
Beringia, the nexus of the northern continents.
Methods
We used approximate B ayesian computation methods to test for simultaneous divergence among eight pairs of taxa, using cytochrome b gene sequences. We calculated coalescence times for eastern and western components of each pair and for the combined pairs, and relate dates to Q uaternary climatic periodicity and combinations of environmental events and physical barriers. Population growth and expansion statistics were used to test evolutionary responses among taxa, including range shifts, persistence or periodic extirpation. Species distribution models ( SDM s) for each taxon were used to predict their geographical ranges during the present interglacial, L ast G lacial M aximum and previous interglacial.
Results
Multiple divergence events across B eringia were primarily coincident with extreme glacial cycles of the late Q uaternary. Structure within B eringia is spatially consistent with at least three environmental barriers arising at different times: the K olyma U plands, B ering S trait and portions of the B ering I sthmus. Levels of divergence varied substantially, indicating evolutionary processes spanning deep and shallow time‐scales. The different demographics among taxa reflect their distinct ecological responses. SDM s predicted regional distributional changes through time and different spatial responses among taxa.
Main conclusions
Beringia predominantly constituted a dispersal corridor during the early Q uaternary and a major centre of endemism in the late Q uaternary. Coincident with severe glacial cycles, small mammal species were ‘caught’ in B eringia and diversified over multiple climatic phases. Relative genetic differentiation across B eringia appears to be related to ecological differences reflecting a gradual adaptation to B eringian environments through time. Some methodological constraints associated with resolving recent (late Q uaternary) isolation events or drawing inferences from a single locus are discussed.
... Miocene/Pliocene) may have resulted in soft allopatric divergences that are temporally congruent, but at a deeper time-scale (e.g. Carstens et al., 2005;Steele et al., 2005). These hypotheses may be further tested using coalescent methods for groups with populationlevel sampling at barriers, either for assessing the temporal congruence of divergence (e.g. ...
... early Pliocene), is also found in numerous temperate terrestrial and marine taxa (e.g. Xiang et al., 2000;Knowles, 2001b;Wares, 2001;Carstens et al., 2005;Steele et al., 2005;Kozak & Wiens, 2006). Processes related to soft allopatric divergence have also long been implicated in refugial speciation dynamics in the Neotropics (e.g. ...
Aim Three common patterns have emerged in comparative phylogeographic analyses at many barriers: (1) a potential geographic pseudocongruence of lineage divergences; (2) a disconnect between the inference of temporally clustered, relatively recent timing for observed speciation events, and dates spanning a broader, apparently random time‐scale; and (3) an apparent prevalence of speciation with recent or continuing gene flow. It is unclear if there is a unifying explanation for these phenomena. We argue that the interaction between geographic barriers to dispersal and ecological limits on the distribution of species can explain these patterns. We suggest that these patterns can be explained by the presence of a continuum between two underlying processes, here termed ‘hard’ and ‘soft’ allopatric divergence, which result from the interplay between organismal ecology and the physioecological nature of geographic barriers.
Location Examples from North America.
Methods We examine comparative phylogeographic divergences in 18 groups of terrestrial vertebrates at two major biogeographic features in North America – the Mississippi River Embayment and the Cochise Filter Barrier – to test predictions made by this hypothesis.
Results We find support for the two distinct processes of hard and soft allopatry, and note several examples exhibiting characteristics of both. Hard allopatry is caused by physical barriers promoting divergence as a function of consistent geographic isolation. Soft allopatry is caused by ecological processes that isolate populations geographically in allopatric refugia through niche conservatism, or across ecological transition zones through niche divergence, but which may be periodic or inconsistent through time.
Main conclusions Viewing geographic speciation as a continuum between hard and soft allopatry can explain all three patterns as a consequence of the physical and ecological mechanisms that isolate populations, and provides an alternative perspective on the impact of ecological factors and physical barriers on lineage formation.
... Phylogeography has also contributed to conservation biology and biodiversity management though characterisation of phylogenetic diversity and endemism, and Evolutionarily Significant Units (Moritz, 1994;Faith et al., 2004;Bryne, 2007;Rosauer et al., 2009). Recent emphasis on hypothesis testing has incorporated coalescent theory and species distribution modelling and has added much needed rigor and ecological realism to the field (Carstens et al., 2005;Carstens & Richards, 2007;Knowles, 2009;Chan et al., 2011;Marske et al., 2013;. Parallels between the disciples of comparative phylogeography and historical biogeography have also long been recognised (Riddle, 1996;Zink, 1996;Arbogast & Kenagy, 2001;Diniz-Filho et al., 2008). ...
... The barrier effect may be particularly pronounced for pond-dwelling species (Mart ınez-Solano et al., 2004), and for species that typically inhabit small streams (Garc ıa-Par ıs & Jockusch, 1999; Alexandrino, Arntzen & Ferrand, 2002). Evolutionary scenarios in which river drainages support dispersal of amphibian species are less frequently documented but some examples are known for semi-or fully aquatic riverine salamanders (Carstens et al., 2005;Jones et al., 2006). ...
We investigated the recent evolutionary history of the Danube crested newt, Triturus dobrogicus through reconstructions of: (1) the number and position of refugia at the last glacial maximum, (2) the role of major central European rivers in pattern of post-glacial dispersal, and (3) the present-day distribution pattern. We analysed sequences of mitochondrial DNA (ND2, 1065 bp) and six microsatellite loci in 363 T. dobrogicus individuals from 58 populations covering the range of the species. Our analyses suggested that T. dobrogicus survived the last glacial maximum in two separate refugia positioned in northwestern Pannonia and in Southern Pannonia from where its range expanded along the Danube and Tisza Rivers. Our findings also confirmed that rivers played an important role in shaping the evolutionary history of amphibian species in Central Europe. We compared the T. dobrogicus range with another lowland amphibian, the fire-bellied toad Bombina bombina, using species distribution modelling. In line with these models, the isolated mountains inside Pannonia are occupied not by B. bombina, but by its mountain-dwelling sister-species B. variegata. However, in contrast to the model, crested newts (including T. dobrogicus) are absent from these mountains. We attribute this biogeographical discrepancy to the positioning of the species’ refugia at the last glacial maximum.
... That is, whereas the field has entered deeply into how genes and lineages evolve, and when lineages can and should be considered as independent, it has not interfaced as intimately with the geographic landscape over which these processes are occurring. Certainly, exceptions are emerging, in which incisive and creative analyses are getting to deeper levels of synthesis linking phylogenetic and phylogeographic pattern to landscapes (Carstens et al. 2005, Carstens & Richards 2007, Edwards et al. 2012. The broadest and deepest of levels of synthesis, however, are perhaps still just over the horizon for this field. ...
We present an overview of the emerging field of species-level distributional ecology, particularly as it relates to phylogeographic studies of birds in Eurasia. This field centers around distributional inferences and predictions deriving from the use of ecological niche modeling. We provide a brief historical review, and then proceed to outline a number of crucial methodological considerations, if models are to have biological meaning and reality. We then proceed to provide a worked example, as well as some thinking about directions in which the field should be moving in terms of questions and approaches
... An exponential growth of plant phylogeographic studies has been observed in Europe and North America in the past two decades, and a similar trend has recently been found in China and adjacent regions [10,11]. Common genetic discontinuities, locations of refuges, and routes of colonisation have been revealed in some regions by comparing phylogeographic structures among species [11][12][13][14][15][16][17][18][19]. In these plant phylogeographic studies, the majority of surveys were conducted on tree species and terrestrial plants, whereas studies on aquatic plants have been relatively scarce [10]. ...
Aquatic vascular plants are a distinctive group, differing from terrestrial plants in their growth forms and habitats. Among the various aquatic plant life forms, the evolutionary processes of freshwater submerged species are most likely distinct due to their exclusive occurrence in the discrete and patchy aquatic habitats. Using the chloroplast trnL-F region sequence data, we investigated the phylogeographic structure of a submerged macrophyte, Hydrilla verticillata, the single species in the genus Hydrilla, throughout China, in addition to combined sample data from other countries to reveal the colonisation and diversification processes of this species throughout the world.
We sequenced 681 individuals from 123 sampling locations throughout China and identified a significant phylogeographic structure (NST > GST, p < 0.01), in which four distinct lineages occurred in different areas. A high level of genetic differentiation among populations (global FST = 0.820) was detected. The divergence of Hydrilla was estimated to have occurred in the late Miocene, and the diversification of various clades was dated to the Pleistocene epoch. Biogeographic analyses suggested an East Asian origin of Hydrilla and its subsequent dispersal throughout the world.
The presence of all four clades in China indicates that China is most likely the centre of Hydrilla genetic diversity. The worldwide distribution of Hydrilla is due to recent vicariance and dispersal events that occurred in different clades during the Pleistocene. Our findings also provide useful information for the management of invasive Hydrilla in North America.
... The separation of AKA/AKW from the rest of the western populations may suggest an isolated coastal refugium, followed by limited gene flow with AKF. Alternatively, an early dispersal event from a Beringian refugium may prove a more probable scenario: the AKA/AKW populations have slightly lower haplotype diversity than AKF (Table 2.5), and contain a subset of haplotypes found in AKF (Table 2 (Soltis et al. 1997;Gavin 2009;Gugger et al. 2010) and amphibians (Carstens et al. 2005) that there was an inland refugium in Idaho. The use of this refugium, or one nearby, has also been discovered in birds (Burg et al. 2006;Krosby & Rohwer 2009) and mammals (Hird & Sullivan 2009). ...
... Climatic oscillations during the Pleistocene have played a significant role in the evolution of the western North American biota by forcing organisms through a series of range contractions and expansions, range shifts, or localized extinctions as glacial ice sheets expanded and retracted [7]. In northwestern North America, refugia are postulated to have occurred in several areas, including Beringia [22][23][24][25], the Chehalis River Valley [4,[26][27][28], the lower Columbia River drainage [29][30][31], the Upper Columbia River drainage [32][33][34][35][36], Haida Gwaii (a.k.a., Queen Charlotte Islands: an archipelago off the Pacific Coast of British Columbia) [37][38][39], and the Klamath-Siskiyou region [5,36,[40][41][42] (Figure 1). Additionally, some taxa have retained genetic signatures of survival in northern and southern refugia along the Pacific Coast [27,43,44]. ...
Background
Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage.
Results
Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas.
Conclusions
Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.
... PAUP* (Swofford 2003) was used to reconstruct each simulated gene tree using parsimony. We then used Mesquite to calculate Slatkin's s statistic, a measure of degree of lineage sorting assuming no postdivergence gene flow, for all observed and simulated trees (Slatkin and Maddison 1989;Carstens et al. 2005). We developed a simple test statistic, the percentage sorted trees (PST) that are reciprocally monophyletic or monophyletic in one haplotype clade with respect to the species tree (s = 1). ...
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation-with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single ev`olutionarily significant unit for conservation purposes.
... Nearly 10 years after Avise (2000) and 20 years after Avise et al. (1987), phylogeography is entering a new and exciting phase. With regard to data analysis, the field is rapidly moving from descriptive methods and into using coalescent models for parameter estimation (Kuhner, 2008), a priori model testing (Beaumont, 2008a;Carstens et al., 2005b;Fagundes et al., 2007), the estimation of spatially-explicit demographic histories (Lemmon and Moriarty Lemmon, 2008), and testing for temporal and/or spatial congruence across codistributed taxa (Carnaval et al., 2009;Hickerson et al., 2006c). Concurrent with these methodological advances will be new ways to visualize phylogeographic data (Kidd and Ritchie, 2006), a rapid growth in genomic phylogeographic data (Townsend et al., 2008;Vera et al., 2008), expansion of taxa included in comparative phylogeographic data sets (Avise, 2008) as well as advances allowing analysis of ancient DNA (Hofreiter, 2008) such that researchers can potentially resolve if humans were the causal agents in the extinction of large mammals at the last glacial maximum rather than climate changes (Barnes et al., 2007). ...
Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro-and macroevolutionary phenomena. The new field was termed phylogeography . Since the ...
... One limitation, however, of relying only on pDNA is their nonrecombinant nature. A given spatial genetic structure inferred by pDNA thus reflects one instance of molecular evolution under a given demographical history whereas simulations have shown that a given demographical history may lead to a wide range of genetic patterns because of the influence of stochastic processes (Carstens et al. 2005;Kuo & Avise 2005). Therefore, the patterns should ideally be confirmed using additional unlinked molecular markers (e.g. ...
Cycles of Quaternary climate change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographic study of rainforest species represents a complementary approach because Pleistocene climate fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri, Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and north-eastern Gabon would have been more affected by past climate change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures.This article is protected by copyright. All rights reserved.
... Upon initial examination, we suspected that this was too high for a species that was compressed into a single Pleistocene refugium. This was in part based on comparisons with vertebrate species such as Plethodon idahoensis and Dicamptodon aterrimus; previous work suggested that these species expanded from small glacial refugia in the northern Rocky Mountains (Carstens et al., 2004(Carstens et al., , 2005a. However, the niche models of Carstens & Richards (2007) imply that the ranges of both P. idahoensis and D. aterrimus were greatly reduced at the LGM, while the range of S. melanopsis was far more extensive. ...
Aim
Coalescent models enable the direct estimation of parameters with clear biological relevance (i.e. divergence time, migration rate and rate of expansion), but they have typically been applied to phylogeographical research without a priori assessment of their fit to the empirical system. Here we explore the extent to which phylogeographical inference can be misled by evaluating the fit of several population genetic models to empirical data collected from the sandbar willow, S alix melanopsis .
Location
The P acific N orthwest mesic forest of N orth A merica.
Methods
We collected sequence data from five loci in 145 individuals. We assessed model fit in: (1) models delimiting previously proposed races within S . melanopsis ; (2) historical biogeographical models, each describing the timing and pattern of diversification; and (3) coalescent models that correspond to those implemented in popular software packages such as IM a , lamarc , and Migrate ‐ n .
Results
We found little evidence for previous hypotheses of cryptic races delimited by habitat type (mesic, lowland or subalpine); rather, our results suggested that these variants originated from the same source population. Historical biogeographical models demonstrate that S . melanopsis has recently expanded from a single refugial population, probably located in the northern Rocky Mountains. An analysis using approximate B ayesian computation indicated that the single population expansion model implemented in lamarc is a better fit to the data than multi‐population models incorporating migration and/or divergence as implemented in Migrate ‐ n and IM a , suggesting that the parameters estimated from the latter are potentially misleading for this system.
Main conclusions
Our research highlights the importance of assessing model fit in addition to estimating parameters to understand evolutionary processes. Taken together, they allow us to infer the historical demography of S . melanopsis in a manner that is not biased by previous work in the system.
... Em 2012, a Filogeografia comemorou 25 anos e entrou em uma fase inovadora. Com relação à análise de dados, ela avançou rapidamente a partir de métodos descritivos para o uso de métodos estatísticos baseados em coalescência (Filogeografia estatística) (KUHNER, 2008), envolvendo testes de modelos a priori (CARSTENS et al., 2005;FAGUNDES et al., 2007). Atualmente, a Filogeografia está se tornando cada vez mais integrativa (AVISE, 2009) (Figura 2). ...
... One half of each filter paper was extracted and the other half was archived as a reserve. We updated the species-specific test described in Goldberg et al. (2011), using the originally utilized cytochrome b data (Nielson et al. 2001; Carstens et al. 2005), to a quantitative PCR test for additional specificity, sensitivity, and quantification abilities (see supplementary data,Table S2 1 , for sequences). Amplicons from each species from each of the four streams used in the test of field methods were sequenced using BigDye Terminator version 3.1 Cycle Sequence Kit (Applied Biosystems) on a 3130xl Genetic Analyzer (Applied Biosystems) to confirm specificity. ...
Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.
... These tests typically are used independently of one another and on relatively inclusive clades sampled over wide geographic extents. Tajima's D (Tajima 1989), for example, is commonly combined with phylogeographic analyses to ask whether major clades show evidence of recent expansion or contraction in effective size (Mahoney 2004; Carstens et al. 2005). Ideally, a composite metric that incorporates the strengths and averages out the weaknesses of a range of the many available tests would provide the most robust inference regarding population demographic history. ...
Systems of geographically isolated habitat patches house species that occur naturally as small, disjunct populations. Many of these species are of conservation concern, particularly under the interacting influences of isolation and rapid global change. One potential conservation strategy is to prioritize the popula-tions most likely to persist through change and act as sources for future recolonization of less stable localities. We propose an approach to classify long-term population stability (and, presumably, future persistence po-tential) with composite demographic metrics derived from standard population-genetic data. Stability metrics can be related to simple habitat measures for a straightforward method of classifying localities to inform conservation management. We tested these ideas in a system of isolated desert headwater streams with mito-chondrial sequence data from 16 populations of a flightless aquatic insect. Populations exhibited a wide range of stability scores, which were significantly predicted by dry-season aquatic habitat size. This preliminary test suggests strong potential for our proposed method of classifying isolated populations according to persistence potential. The approach is complementary to existing methods for prioritizing local habitats according to diversity patterns and should be tested further in other systems and with additional loci to inform composite demographic stability scores.
... Using coalescent models to test alternative hypotheses Coalescent models have proved to be a useful tool for phylogeographic research even in the absence of explicit reconstructions of species past ranges (e.g. Milot et al., 2000;Knowles, 2001;Carstens et al., 2005b;DeChaine & Martin, 2005;Russell et al., 2005;Steele & Storfer, 2006). For example, using a statistical evaluation of five separate potential population models, Steele & Storfer (2006) were able to show that populations of Pacific giant salamander (Dicamptodon tenebrosus) were isolated in separate glacial refugia during the Pleistocene glaciation. ...
Statistical phylogeographic studies contribute to our understanding of the factors that influence population divergence and speciation, and that ultimately generate biogeographical patterns. The use of coalescent modelling for analyses of genetic data provides a framework for statistically testing alternative hypotheses about the timing and pattern of divergence. However, the extent to which such approaches contribute to our understanding of biogeography depends on how well the alternative hypotheses chosen capture relevant aspects of species histories. New modelling techniques, which explicitly incorporate spatio-geographic data external to the gene trees themselves, provide a means for generating realistic phylogeographic hypotheses, even for taxa without a detailed fossil record. Here we illustrate how two such techniques - species distribution modelling and its historical extension, palaeodistribution modelling - in conjunction with coales- cent simulations can be used to generate and test alternative hypotheses. In doing so, we highlight a few key studies that have creatively integrated both historical geographic and genetic data and argue for the wider incorporation of such explicit integrations in biogeographical studies.
... The disjunct distributions of a large array of organisms in the widely separated coastal and inland wetbelt regions of northwestern North America ( Fig. 1) have been studied by researchers in both the United States and Canada. This distribution has been highlighted among plants (Leiberg 1900;Schofield 1969;Johnson and Steele 1978;Lorain 1988;Schofield 2004), lichens (Goward and Spribille 2005), and animals (Wilke and Duncan 2004;Carstens et al. 2005a;Carstens et al. 2005b). Until recently, most researchers assumed these disjunctions are such that coastal regions were the geographical source and inland regions the sink. ...
A region of contrastively wetter and milder climate occurs in inland northwest North America, separated from similar climates of the Pacific coast by 200400km. Researchers have long noted that numerous vascular plants divide their ranges between the interior wetbelt and coastal regions, although many such disjunctions have hitherto gone undocumented. Here I summarize all vascular plants shared between coastal and interior wetbelt regions, disjunct by at least 200km. These disjunct taxa are assigned to north-coast and south-coast lists according to whether the coastal portions of the ranges occur primarily north or south of the southern limits of maximum continental glaciation. A list of interior wetbelt endemic taxa is also presented, focusing on those that occur at forested elevations. Presence/absence for coastal disjunct and endemic taxa were assigned to grid of 1 1 latitudelongitude cells. Using this grid, concentrations of disjunct and endemic taxa were detected, and total values per cell were tested in linear regression for a relationship to mean annual precipitation. In total, 116 coastal disjunct taxa were detected, 31 of them north-coastal and 85 south-coastal. Interior wetbelt endemic and subendemic taxa total 95, and of these, 46 were found primarily at forested elevations. North-coast taxa were found over a wide latitudinal range both north and south of the glacial limits, and their distribution had a weak positive relationship with annual precipitation. South-coast and endemic taxa were found mostly south of the glacial limits, and their distribution did not correlate to annual precipitation. The greatest concentrations of south coastal disjunct and endemic taxa occurred in the Clearwater region of north-central Idaho; a region noted by previous researchers to be a likely ice-age refugium for wet-climate dependent plants and animals. Inferences are made from these patterns, both for biogeographical understanding of the roles played by the interior wetbelt and some regions connecting to the coast, as well as for preservation of biodiversity and ecosystem continuity.
... Here, we used model selection to identify an effective spatial scale to manage a stream salamander species, Dicamptodon aterrimus (Idaho Giant Salamander), which is listed as a species of concern in the northern Rocky Mountains. Little is known about D. aterrimus, but available information suggests that its distribution is patchy across and within stream drainages (Carstens et al., 2005). In the region where D. aterrimus occurs, many stream drainages have undergone timber harvest and road building, anthropogenic disturbances that can reduce habitat quality within streams and reduce population connectivity among streams (Carr and Fahrig, 2001;Fagan, 2002). ...
Species distribution and abundance depend on a balance between local and landscape-scale processes. To successfully manage populations in regions with anthropogenic disturbances and habitat fragmentation, an understanding of important processes at each of these spatial scales is important. We used a model selection approach to identify an effective spatial scale to manage the Idaho Giant Salamander, Dicamptodon aterrimus. We used data from field surveys to compare support for local and landscape-scale models that explain D. aterrimus occurrence and density in 40 streams distributed throughout the Lochsa River basin, Idaho. Local-scale models included covariates that reflect patch quality. Landscape-scale models included variables that reflect predictions from metapopulation theory about the importance of patch size, connectivity, and fragmentation. Our results suggest that landscape-scale processes are important controls on D. aterrimus occurrence and that this species has broad habitat requirements within streams. Specifically, we found that probability of D. aterrimus occurrence was highest in roadless drainages and lowest in spatially isolated streams and in drainages with high old-growth forest density. Surprisingly, we found that D. aterrimus density was greatest in streams with a high proportion of embedded substrate and fine sediment. The positive association with embedded substrate may reflect adaptation to a high frequency of natural disturbances, such as landslides, in our study area. We suggest that management and conservation efforts for this species focus on protecting roadless areas and restoring stream connectivity in human-impacted areas, rather than on only improving habitat quality within streams.
... One of the most relevant findings of this study is related with the genetic distinctiveness of the BC Revelstoke and Idaho populations . Despite the small sample size and the lack of microsatellite data, this highlights the importance of southern BC and Idaho as a potential refugium for animals and plants [11,49,50,51]. Although our data (genetics and SDM) do not allow us to conclusively state a refugia in the northern Rocky mountain area (such as Clearwater), it is congruent with a widespread pattern where populations southern of the ice sheets are genetically more diverse (see also Missouri and Louisiana populations,Table 1) than their northern counterparts [28,52]. ...
The glacial cycles of the Pleistocene have been recognized as important, large-scale historical processes that strongly influenced the demographic patterns and genetic structure of many species. Here we present evidence of a postglacial expansion for the Downy Woodpecker (Picoides pubescens), a common member of the forest bird communities in North America with a continental distribution. DNA sequences from the mitochondrial tRNA-Lys, and ATPase 6 and 8 genes, and microsatellite data from seven variable loci were combined with a species distribution model (SDM) to infer possible historical scenarios for this species after the last glacial maximum. Analyses of Downy Woodpeckers from 23 geographic areas suggested little differentiation, shallow genealogical relationships, and limited population structure across the species' range. Microsatellites, which have higher resolution and are able to detect recent differences, revealed two geographic groups where populations along the eastern edge of the Rocky Mountains (Montana, Utah, Colorado, and southern Alberta) were genetically isolated from the rest of the sampled populations. Mitochondrial DNA, an important marker to detect historical patterns, recovered only one group. However, populations in Idaho and southeast BC contained high haplotype diversity and, in general were characterized by the absence of the most common mtDNA haplotype. The SDM suggested several areas in the southern US as containing suitable Downy Woodpecker habitat during the LGM. The lack of considerable geographic structure and the starburst haplotype network, combined with several population genetic tests, suggest a scenario of demographic expansion during the last part of Pleistocene and early Holocene.
... Ecological niche modeling and their projections onto paleoclimatic scenarios offer one important means of enriching these views into the past. These multiple lines of evidence will provide a much richer view of biogeographic history, as has become evident from the success of first steps in this direction (Carstens et al. 2005, Cheddadi et al. 2006, Carstens and Richards 2007, Knowles et al. 2007, Alsos et al. 2009 , Waltari and Guralnick 2009). Neil Burgess: Yes, biogeography is relevant to my work. ...
... When there is no gene flow among populations, as is the case in A. poncensis and A. cooki, the S statistic measures the degree of lineage sorting, and can be used to test different spatial and temporal hypotheses of population histories (for example, Carstens et al., 2005;Spellman & Klicka, 2006;Steele & Storfer, 2006). The S statistic for the empirical gene genealogy of A. poncensis was S = 4, and that for A. cooki was S = 5. ...
Comparative phylogeography is a powerful method for testing hypotheses of evolutionary diversification in ecological communities. Caribbean lizards of the genus Anolis are a species-rich group and a well-known example of adaptive radiation. In 1983, Ernest Williams suggested that species of Anolis that belong to the same ‘climate type’ (taxa that occur sympatrically in either xeric, mesic or very wet habitats) probably evolved under similar ecological conditions, and thus have experienced a parallel evolutionary history. This hypothesis implies that the phylogeographical patterns of such species can be expected to be concordant, a prediction that has not been tested. We conducted a comparative phylogeographical and population genetic study of Anolis poncensis and Anolis cooki, two sympatric lizards restricted to the aridlands of southwestern Puerto Rico, to determine whether there are similarities in the genetic architecture of the two anoles that may have resulted from a parallel response to the same historical events, or whether each taxon displays a distinct pattern of geographical distribution of intraspecific genealogical lineages. Our dataset consisted of approximately 2120 base pairs of the ND2 and cytochrome b genes from specimens from the known extant populations of the two species. The average haplotype diversity in A. poncensis (0.36) was considerably lower than that in A. cooki (0.62), whereas the average nucleotide diversity in A. cooki was ten times higher than that in A. poncensis. Both anoles showed pronounced phylogeographical structure, with no shared haplotypes among populations. The gene genealogy of A. poncensis recovered three strongly supported clades: the westernmost population, the easternmost deme and the three intermediate populations. In A. cooki, the populations from the western part of the species' range formed a well-supported group, to the exclusion of the eastern demes. Pairwise FST values revealed significant genetic differentiation among all conspecific populations of both anoles. Coalescent simulations indicated that A. poncensis could have evolved under a scenario of simple population fragmentation during the Pleistocene, but that A. cooki did not. The estimate of the effective population size of A. cooki was an order of magnitude larger than that of A. poncensis. Because time to the most recent common ancestor is dependent on effective population size, this tenfold difference implies that the time to the most recent common ancestor of A. cooki is much longer than that of A. poncensis, which indicates that A. cooki diversified earlier than A. poncensis. Collectively, these findings suggest that, although A. poncensis and A. cooki are syntopic throughout much of their current distribution, intraspecific diversification in the two species has not proceeded in parallel, which does not support the hypothesis that Anolis lizards that occupy the same climate-type region possess spatially and temporally congruent genetic architectures. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 617–634.
... However, due to the difficulties associated with using MDIV with data from more than two species, we regard the Dicamptodon estimate as tentative. Additionally, in each lineage there is evidence of post-Pleistocene expansion from refugial populations (Nielson et al. 2001;Carstens et al. 2004Carstens et al. , 2005, as predicted if these taxa persisted in NRM glacial refugia during the Pleistocene. ...
Abstract We examine the evolution of mesic forest ecosystems in the Pacific Northwest of North America using a statistical phylogeography approach in four animal and two plant lineages. Three a priori hypotheses, which explain the disjunction in the mesic forest ecosystem with either recent dispersal or ancient vicariance, are tested with phylogenetic and coalescent methods. We find strong support in three amphibian lineages (Ascaphus spp., and Dicampton spp., and Plethodon vandykei and P. idahoensis) for deep divergence between coastal and inland populations, as predicted by the ancient vicariance hypothesis. Unlike the amphibians, the disjunction in other Pacific Northwest lineages is likely due to recent dispersal along a northern route. Topological and population divergence tests support the northern dispersal hypothesis in the water vole (Microtus richardsoni) and northern dispersal has some support in both the dusky willow (Salix melanopsis) and whitebark pine (Pinus albicaulis). These analyses demonstrate that genetic data sampled from across an ecosystem can provide insight into the evolution of ecological communities and suggest that the advantages of a statistical phylogeographic approach are most pronounced in comparisons across multiple taxa in a particular ecosystem. Genetic patterns in organisms as diverse as willows and salamanders can be used to test general regional hypotheses, providing a consistent metric for comparison among members of an ecosystem with disparate life-history traits.
... Objective tests of the scenarios resulting from the population genetic and nested clade approaches were performed in order to evaluate support for the phylogeographic models (Knowles & Maddison, 2002). Coalescent simulations of genealogies constrained within models of population divergence provide a powerful means of assessing how well observed genetic patterns fit phylogeographic hypotheses (Knowles, 2001; Carstens et al., 2005). We tested two general models of population divergence to determine whether observed patterns in C. meadii and P. smintheus were consistent with the null hypothesis of fragmentation from a single, ancestral population (Fig. 1b) or differentiation in three refugia and if divergence times were concordant between the two species. ...
Aim We inferred the phylogeography of the alpine butterfly Colias meadii Edwards (Pieridae) and compared its genetic structure with that of another high elevation, co‐distributed butterfly, Parnassius smintheus Doubleday (Papilionidae), to test if the two Rocky Mountain butterflies responded similarly to the palaeoclimatic cycles of the Quaternary.
Location Specimens were collected from 18 alpine sites in the Rocky Mountains of North America, from southern Colorado to northern Montana.
Methods We sequenced 867 and 789 nucleotides of cytochrome oxidase I from an average of 19 and 20 individuals for C. meadii and P. smintheus , respectively, from each of the same 18 localities. From the sequence data, we calculated measures of genetic diversity within each population (H, θ ), genetic divergence among populations ( F ST ), and tested for geographic structure through an analysis of molecular variance ( amova ). Population estimates were compared against latitude and between species using a variety of statistical tests. Furthermore, nested clade analysis was implemented to infer historic events underlying the geographic distribution of genetic variation in each species. Then, we compared the number of inferred population events between species using a nonparametric Spearman's rank correlation test. Finally, we ran coalescent simulations on each species’ genealogy to test whether the two species of Lepidoptera fit the same model of population divergence.
Results Our analyses revealed that: (1) measures of within‐population diversity were not correlated with latitude for either species, (2) within‐site diversity was not correlated between species, (3) within a species, nearly all populations were genetically isolated, (4) both species exhibited significant and nearly identical partitioning of genetic variation at all hierarchical levels of the amova , including a strong break between populations across the Wyoming Basin, (5) both species experienced similar cycles of expansion and contraction, although fewer were inferred for C. meadii , and (6) data from both species fit a model of three refugia diverging during the Pleistocene.
Main conclusions While our findings supported a shared response of the two butterfly species to historic climate change across coarse spatial scales, a common pattern was not evident at finer spatial and temporal scales. The shared demographic history of the two species is consistent with an expanding–contracting archipelago model, suggesting that populations persisted across the geographic range throughout the climate cycles, experiencing isolation on ‘sky islands’ during interglacial periods and becoming connected as they migrated down‐slope during cool, wet climates.
... Two pronounced patterns within the H. oregonensis dataset can be conWdently associated with geographic features in the NE PaciWc. While the combination of a nonragged mismatch distribution and negative Tajima's D is a common signature of expansion from a glacial refugium (Carstens et al. 2005; Marko 2004), a number of points cast doubt on a simple scenario of northward expansion from a southern population. Each California subpopulation south of Cape Blanco shares a signature pattern of these indices which contrasts with that of northern subpopulations. ...
Discrete estuary subpopulations of the mud crab Hemigrapsus oregonensis (Dana, 1851) are connected via larval dispersal. Sequence variation at the mtDNA COI locus was examined in eight populations
sampled in 2001–2002 from central California through northern Oregon in the northeast Pacific (36.6–45.8°N) to infer patterns
of dispersal and historical connectivity in the region. Strong evidence for persistence since the mid-Pleistocene, with no
range truncation resulting from southward shifting temperature isoclines, was provided by a phylogeographic pattern of haplotypes
of an older clade distributed throughout the sampled range. A recently derived clade became widespread only north of Cape
Blanco after the last glacial maximum. Its clear pattern of restriction to the northern area, in the absence of similarly
restricted southern clades, suggests that contemporary dispersal around Cape Blanco is rare (population F
ST=0.192). Low pairwise differentiation within Oregon and within central California, as well as contrasts between northern
and southern groups in the shape of the pairwise mismatch distribution, nucleotide diversity, and Tajima’s D suggest that these regions reflect different demographic histories. Potential mechanisms explaining this latitudinal break
include contemporary coastal circulation patterns, selection, and ancient patterns of larval dispersal in the California Current.
... We amplified the mitochondrial control region (CR) and the protein coding cyt b gene because they are two of the most rapidly evolving markers in the mitochondrial genome of fishes (Broughton and Reneau, 2006), and have proven to be useful in determining phylogenetic relationships and in detecting phylogeographic patterns that stem from Neogene events in many western North American taxa (e.g., Nielson et al., 2001;Dowling et al., 2002;Johnson, 2002;Carstens et al., 2004Carstens et al., , 2005bJohnson et al., 2004;Mock and Miller, 2005;Steele et al., 2005;Mock et al., 2006). We amplified CR using primers L-Pro and MRT-2 ( Meyer et al., 1994;Ptacek and Breden, 1998) and cyt b using HA-a and LA-a (Dowling and Naylor, 1997). ...
Diversification of many North American taxa, including freshwater fishes, has been heavily influenced by the effects of complex geological and climatic events throughout the Cenozoic that have significantly altered the landscape. Here, we employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. We also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within the group. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and Richardsonius, with Clinostomus being sister to an Iotichthys–Richardsonius clade, hence the currently recognized sister relationship between Clinostomus and Richardsonius is not supported. These genera appear to be monophyletic lineages, and sister species within genera appear to be reciprocally monophyletic. The two species within the genus Richardsonius both exhibit phylogeographic structure that is worthy of further investigation. Divergence time estimates between genera and species are Miocene or Pliocene in age, and divergence between phylogroups within species occurred in the late Pliocene to Pleistocene. These splits coincide with documented geological and climatic events.
... Alternative species-history models are reflected in different branching pattern of gene trees (Knowles & Maddison 2002). Consequently, discordance between species-histories and gene trees could be employed to evaluate the relative support of alternative models (Knowles 2001(Knowles , 2004Knowles & Maddison 2002;Bailey et al. 2005;Carstens et al. 2005;Steele & Storfer 2006;Knowles et al. 2007). A common measure of discordance is the Slatkin & Maddison (1989)'s S statistics, which measures the number of additional parsimony steps in a given tree that are needed for the gene tree to correspond to the population ⁄ species history in which it is contained (Knowles 2001;Bailey et al. 2005). ...
Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence-based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species-history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 and 1.57 Ma. When empirical data were compared to coalescence-based simulated distributions of discordance and p-distance statistics, two species-history models were chosen in which the first branching lineage derived in Canarian Festuca agustinii. Its sister lineage could have involved a recent polytomy leading to the Madeiran Festuca jubata, the Azorean Festuca francoi + Festuca petraea and the continental Festuca rivularis lineages (Canarian model) or the sequential branching of lineages leading to F. jubata and finally to the sister clades of F. rivularis and F. francoi + F. petraea (Sequential model). Nested clade phylogeographic analysis (NCPA) and a first adapted host-parasite co-evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long-distance colonizations for the entire diploid red Festuca complex, but allopatric-fragmentation and isolation-by-distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a stepping-stone model at all hierarchical levels. Maximum-likelihood-based dispersal-extinction-cladogenesis (DEC) models were superimposed on the Sequential model species tree. The three-independent-colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.
... We used coalescent simulations of genealogies constrained within models of population divergence to assess the fit of observed gene tree to different phylogeographic hypotheses (Knowles, 2001;Knowles & Maddison, 2002;Carstens et al., 2005;DeChaine, 2008). Hypothesis testing was performed using the software MESQUITE, version 2.5 (Maddison & Maddison, 2008). ...
Increasing evidence suggests that geological or climatic events in the past promoted allopatric speciation of alpine plants in the Qinghai-Tibetan Plateau and adjacent region. However, few studies have been undertaken to examine whether such allopatric divergences also occurred within a morphologically uniform species. In the present study, we report the evolutionary history of an alpine shrub species, Hippophae tibetana, based on examining chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variations. We sequenced two cpDNA fragments (trnL-F and trnS-G) and the nuclear ITS region in 183 individuals collected from 21 natural populations. Ten chlorotypes and 17 ITS types were identified. Phylogenetic analyses of both chlorotypes and ITS sequence variations suggested two distinct lineages distributed in the eastern and western region, respectively. On the basis of the fast and low plant substitution rates, these two lineages were estimated to have diverged from each other between 1 and 4 million years ago, during the period of the major glaciations and orogenic processes. In addition, ITS has undergone the accelerated evolution in two populations in the southern Himalaya isolated by the high mountains with a surprising accumulation of the private variations. The east–west split was also supported by an analysis of molecular variance, which partitioned around 91% of the total cpDNA variance between these two groups of populations. A single chlorotype was found for most populations in eastern or western region, suggesting a recent postglacial expansion within each region. Star-phylogeny and mismatch analyses of all chlorotypes within the eastern group of populations suggested an earlier regional expansion before the Last Glacial Maximum (LGM). The local fixture of the different chlorotypes in multiple populations suggested more than one refugia remained for eastern or western region. Coalescent tests rejected the hypothesis that all current populations originated from a single refugium during the LGM. Instead, they supported hypothesis that two lineages diverged before the late Pleistocene. These findings, when taken together, suggested that this species had experienced long allopatric divergence and recent regional range expansions in response to orogenic processes and the climate changes. The evolutionary history of this shrub species highlights importance of geographical isolations to the intraspecific divergence of alpine plants occurring in the world's ruff. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 37–50.
... All showed disjunct modern distributions spanning the Cascades and Rocky-Mountains, but genetic data suggest that these species achieved their current range in different ways. Some maintained separate populations in each mountain range throughout the last glacial, while others recently expanded from distinct glacial refugia [11,171819. Even within communities showing largely concordant phylogeographic patterns , species displaying exceptional histories are frequent [4,20]. ...
Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community--Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes.
... Density survey and water sample collections were made during base flow, measured as 0.23 m 3 s 21 , in the study stream. We designed a set of species-specific primers for each species targeting a small region of the mitochondrial DNA (mtDNA) cytochrome b gene (obtained from GenBank) [24,25] (Table 2). The distribution of these two species is disjunct from their congeners along the Pacific coast to the west; therefore, we designed primers to be species-specific within our system (the northern Rocky Mountains region) but also to detect the congeners of each species for wider geographic applicability. ...
Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.
The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide, and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (S. zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The Continental Divide is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.
In northern Idaho ( USA ), more than 100 vascular plant species are disjunct >160 km from their main distribution along the Pacific Northwest coast. It remains unclear whether most species within this interior forest disjunction, including Tsuga mertensiana , survived the last glacial period in a north‐Idaho refugium or whether these species colonized the region via long‐distance dispersal during the Holocene.
Sediment cores were extracted from three mid‐ to high‐elevation lakes within T. mertensiana ‐dominated forests in the Northern Rocky Mountains of Idaho. Pollen and macrofossils were used to reconstruct forest composition, determine the timing of T. mertensiana establishment, examine the hypothesis that the region was a glacial refugium, and contrast how climate, competition and/or dispersal limitation have influenced its modern distribution.
The modern distribution of T. mertensiana was analysed by constructing a range map and modelling the potential species distribution. The presence of outlier populations surrounding the Idaho disjunction along with broad areas of unoccupied suitable habitat indicates that the range of T. mertensiana is currently expanding. To assess the accuracy of T. mertensiana pollen at detecting its range limit, a network of pollen surface samples was used to analyse the probability of detecting T. mertensiana pollen as a function of distance from its geographical range limit. Consistent T. mertensiana pollen occurrence at ≥1% abundance is likely only within 42 km of its range limit.
Tsuga mertensiana first appears in the pollen and macrofossil record at the highest‐elevation site at c . 4,100 cal year bp , then at the next highest‐elevation site at c . 1,600 cal year bp , and last at the mid‐elevation site at 800 cal year bp . Tsuga mertensiana pollen occurs continuously at ≥1% at all three sites by c . 300 cal year bp suggesting regional presence. The timing of arrival suggests that T. mertensiana is a recent component of the forests of Idaho, having arrived during the Holocene via long‐distance dispersal from coastal populations over 160 km away.
Synthesis . Comparison with palaeoclimate reconstructions from the broader region suggests that climate was a greater limiting factor than dispersal in the Holocene establishment in the interior, indicating little difficulty overcoming a large dispersal barrier. However, T. mertensiana remained at low abundances for millennia until Little Ice Age climates promoted its recent increase in abundance. Unoccupied areas of suitable habitat suggest that competition, rather than climate or dispersal, is a limiting range infilling in the interior mesic forests today.
We describe the range-wide phylogeography of Blackpoll Warblers (Setophaga striata), a migratory passerine with a broad breeding range in North America's boreal forest that encompasses several possible biogeographic barriers but shows no phenotypic geographic variation. We used mitochondrial control-region sequences from 304 individuals in combination with ecological niche models and coalescent simulations to test alternative historical hypotheses about the number of Pleistocene refugial populations and divergences among modern populations. Population pairwise F-ST. and spatial analyses of molecular variance suggested significant genetic structure among western, eastern, and Newfoundland populations, but no structure among sky-island populations at the southeastern periphery of the breeding range. Inferred gene flow fits a model of isolation-by-distance. Coalescent simulations rejected all multiple-refugia hypotheses in favor of a single refugium. Paleodistribution models and modern migratory pathways suggested that the refugium was located in southeastern North America. In contrast to previous studies that have invoked multiple Pleistocene refugia as the cause of genetic structure in North American bird species, our analyses suggest that geographic structure in Blackpoll Warblers results from isolation-by-distance rather than a history of sundered populations. Received 23 November 2011, accepted 20 March 2012.
... Phylogeographical studies are also emerging for plants occurring in once-glaciated and arctic eastern North America (eg ... (2003). Aix sponsa, wood duck, mt DNA seq, E–W North America , but no structure in E NA, parsimony network, not given, Peters et al. (2005). ...
The population genetic structure of many high-latitude species in North America was affected by the last glaciation, and current structure reflects isolation in refugia and colonisation patterns. Large ice-free areas, both south of the ice sheets and in the north-west, supported numerous flora and fauna throughout this period. Fossil evidence suggests additional western glacial refugia existed both on Haida Gwaii (the Queen Charlotte Islands) and in northern Idaho. The chestnut-backed chickadee Poecile rufescens is a songbird found along the western edge of Canada and the United States, with a linear distribution along the coast, and an isolated interior population. Mitochondrial DNA sequence data (control region and ATPase 6-8) from 10 populations (n = 122) were used to test for population genetic structure. The data supported a general north/south separation. Haida Gwaii was found to be genetically distinct from the rest of the populations, and the two northern British Columbia populations separated from all but Alaska. The interior population showed evidence of both historical isolation and secondary colonisation by birds from coastal populations. Neutrality tests suggested a past population expansion in all populations from previously glaciated areas, and a stable population in areas believed to be unglaciated. This pattern supports the use of multiple glacial refugia by the chestnut-backed chickadee. We could not reject the use of Haida Gwaii or the interior (i.e. Clearwater Basin) as glacial refugia.
Although the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curcu-lionidae), is a devastating pest in the United States and Mexico, its population structure and genetic diversity in Mexico on wild and cultivated cotton hosts (genus Gossypium) is poorly understood. Past studies using morphology, host use, and distribution records suggest that A. grandis grandis comprises three forms with host-associated characteristics: the southeastern form (from domesticated Gossypium hirsutum L., southeastern United States and northeastern Mexico), the thurberia form (from Gos-sypium thurberi Todaro, Arizona and northwestern Mexico), and the Mexican form (from multiple Gossypium species and other malvaceous plant genera in the remainder of Mexico and Central America). However, the phylogenetic relationships, host preferences, and distributions of these forms are not completely understood. An alternative hypothesis of an eastern and western form of the boll weevil is suggested by the suspected phylogeographic range expansion from an ancestral distribution in the tropics northward along both Mexican coasts, culminating in the maximally contrasting phenotypes observed in the northeastern and northwestern arms of the current distribution. In this study, we sequenced one mitochondrial and four nuclear genes to gain insight into the evolutionary relationships among the putative forms and their distributions on wild and domesticated cotton hosts. Using models of evolution, we compared the three-form to the two-form classiÞcation and to two alternative classiÞcations that incorporate geography and host use traits. The genetic data at most loci provide stronger support for the two-form than the three-form hypothesis, with an eastern and western group separated by the Sierra Madre Occidental mountain range. They do not support separate taxonomic status for boll weevils developing on G. thurberi.
Background: Evidence strongly suggests that Beringia was a refugium for tundra taxa throughout the Quaternary (the last 2 million years). However, the genetic consequences of the repeated formation and flooding of the Bering Land Bridge remain uncertain.Aims: The goal of this paper was to determine the role that the unique environmental history of Beringia played in the diversification of tundra flora.Methods: I adopted a comparative coalescent approach to test models of divergence for arctic flora within Beringia. The literature was surveyed for phylogeographic studies that sampled broadly across the region and incorporated molecular markers appropriate for coalescent analyses. Of the 13 possible taxa, only two fit these criteria: Saxifraga oppositifolia (Saxifragaceae) and Vaccinium uliginosum (Ericaceae). Observed gene trees were compared with a distribution of trees simulated under neutral coalescence to test models of population divergence. Population models fell within two major categories reflecting the importance of either the Bering Land Bridge or the Bering Sea dispersal barrier on the distribution of genetic diversity in the species.Results: Both species fit ‘bridge’ models, but S. oppositifolia supported a model of eastward migration while V. uliginosum fits a unified Beringia refugium model. The evolutionary implications of these findings are discussed.Conclusions: The limited number of studies emphasises the need for more sequence-based research in the region. This will help resolve the history of the Beringia tundra ecosystem, which has important implications for the diversification of tundra flora, the history of Beringia, and the potential consequences of climate change on the distribution of biological diversity.
For northern taxa, persistence in multiple vs. single Pleistocene refugia may have been an important determinant of contemporary range size, with larger ranges achieved by species that colonized the north from several glacial refugia. Under this hypothesis, widespread species are expected to demonstrate marked phylogeographic structure in previously glaciated regions. We use a genome-wide survey to characterize genetic structure and evaluate this hypothesis in the most widely distributed salamander in the Pacific Northwest, the long-toed salamander (Ambystoma macrodactylum). Patterns of variation based on 751 amplified fragment length polymorphism (AFLP) loci and mitochondrial sequence data were concordant and support the recognition of at least four distinct lineages of long-toed salamander. The distributions of these lineages indicate that multiple refugia contributed to the species' large contemporary range. At the same time, with up to 133 AFLP bands differing between lineages and levels of sequence divergence ranging from 2.5 to 5.8%, these lineages would be considered separate species by some definitions. Such splitting would partition the large geographic range of the long-toed salamander into several relatively restricted ranges. Our results thus also underscore the potential for estimates of geographic range size to vary considerably depending on the taxonomic treatment of cryptic lineages.
Contemporary distribution of North American species has been shaped by past glaciation events during the Quaternary period. However, their effects were not as severe in the southern Rocky Mountains and Northern Mexico as elsewhere in North America. In this context, we test hypotheses about the historical demography of Dendroctonus pseudotsugae, based on 136 haplotypes of mitochondrial cytochrome oxidase I. The phylogenetic analysis yielded four haplogroups corresponding to northwestern United States and southwestern Canada (NUS), southwestern United States (Arizona, SUS), northwestern Mexico (Sierra Madre Occidental, SMOC), and northeastern Mexico (Sierra Madre Oriental, SMOR). Predictions of demographic expansion were examined through neutrality tests against population growth and mismatch distribution. Results showed that the NUS and SMOC haplogroups have experienced demographic expansion events, whereas the SUS and SMOR haplogroups have not. Divergence times between pairs of haplogroups were estimated from early to middle Pleistocene. The longer divergence time between NUS and all other haplogroups could be the result of refugia within the Pacific Northwest and northern Rocky Mountains and long-term isolation from southernmost populations in Mexico. The results obtained in this study are in agreement with the evolutionary history of the host Douglas-fir, as the warmer climates of interglacial periods pushed conifers northward of Colorado, New Mexico, and Arizona, whereas environmental changes reduced the population size of Douglas-fir and forced fragmentation of distribution range southward into northern Mexico.
We present Ginkgo, a software package for agent-based, forward-time simulations of genealogies of multiple unlinked loci from diploid populations. Ginkgo simulates the evolution of one or more species on a spatially explicit landscape of cells. The user of the software can specify the geographical and environmental characteristics of the landscape, and these properties can change according to a prespecified schedule. The geographical elements modelled include the arrangement of cells and movement rates between particular cells. Each species has a function that can calculate a fitness score for any combination of an individual organism's phenotype and environmental characteristics. The user can control the number of fitness factors (the dimensionality of the cell-specific fitness factors and the individuals phenotypic vectors) and the weighting of each of these dimensions in the fitness calculation. Cell-specific fitness trait optima can be specified across the landscape to mimic differences in habitat. In addition to their differing fitness functions, species can differ in terms of their vagility and fecundity. Genealogies and occurrence data can be produced at any time during the simulation in NEXUS and ESRI Ascii Grid formats, respectively.
MrBayes is a program for the Bayesian inference of phylogeny. This manual explains Bayesian inference of phylogeny and how to use the program. The program has a command-line interface and should run on a variety of computer platforms. Note that the computer should be reasonably fast and should have a lot of memory (depending on the size of the data matrix, the program may require hundreds of megabytes of memory). The program is optimized for speed and not for minimizing memory requirements. This manual is divided into two parts. The first section gives an overview of the program with a brief tutorial to help you get started and the second section introduces Bayesian inference and presents some of the theory behind the program. Conventions used in this manual What you see on the screen and what is in the input file is in a sans serif font. What you type is in a bold font.
Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
Various methodological approaches using molecular sequence data have been developed and applied across several fields, including phylogeography, conservation biology, virology and human evolution. The aim of these approaches is to obtain predictive estimates of population history from DNA sequence data that can then be used for hypothesis testing with empirical data. This recent work provides opportunities to evaluate hypotheses of constant population size through time, of population growth or decline, of the rate of growth or decline, and of migration and growth in subdivided populations. At the core of many of these approaches is the extraction of information from the structure of phylogenetic trees to infer the demographic history of a population, and underlying nearly all methods is coalescent theory. With the increasing availability of DNA sequence data, it is important to review the different ways in which information can be extracted from DNA sequence data to estimate demographic parameters.
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.
A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.
The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing
and the availability of efficient computer programs to perform phylogenetic analyses. The application of computer simulation
and likelihood ratio tests to evolutionary hypotheses represents a recent methodological development in this field. Likelihood
ratio tests have enabled biologists to address many questions in evolutionary biology that have been difficult to resolve
in the past, such as whether host-parasite systems are cospeciating and whether models of DNA substitution adequately explain
observed sequences.
The phylogeography of Sumichrast's harvest mouse (Reithrodontomys sumichrasti) was examined through maximum-likelihood and parsimony analyses of 1,130 bp of mitochondrial Cytochrome b sequence data from 43 individuals. The phylogeography of this Middle American highland forest-dwelling species was compared to that previously published for the codistributed Aztec deer mouse complex (Peromyscus aztecus/Peromyscus hylocetes complex) in order to test competing hypotheses of concerted versus independent responses of codistributed forms to past climatic fluctuations. Qualitatively, there were strong similarities in the phylogeographic patterns of the two groups, yet there were also areas of incongruence. Likelihood-ratio tests (Kishino-Hasegawa-Templeton and parametric bootstrap tests) indicated that this incongruence is significant and cannot be attributed simply to uncertainty in phylogenetic estimation, thereby falsifying the concerted-response hypothesis. Conversely, tree-reconciliation analysis of the area relationships inferred for each group separately indicated that there has been a significant history of covicariance between the two groups, falsifying the independent-response hypothesis. It appears that codistributed taxa in the geologically complex highlands of Mesoamerica share more common biogeographical history than can be accounted for by the independent-response hypothesis yet have not responded to past climatic fluctuations in the lock-step fashion predicted by the concerted-response hypothesis.
Keywords:cladogram estimation;gene genealogy;phylogeography;population genetics;software
As progress in cell developmental biology carries on at a breakneck speed, new techniques constantly arise to plug the gaps left by traditional strategies. Cellular Interactions in Development provides detailed discussion and protocols of some of these new techniques, which allow the manipulation of developing organisms such as Drosophila or plants, when and where cells interact with each other to influence their development. The book looks at the really exciting innovations of the identification and functional test of molecules which control these cellular behaviours. The book also describes a number of new ways of hunting for these important proteins involved in cellular communication. A fully comprehensive manual which will prove indispensable to researchers in the fields of cell, developmental, and molecular biology.
A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.
We present a phylogenetic analysis of the Ambystoma tigrinum complex, based on approximately 840 base pairs of mitochondrial-DNA sequence from the rapidly evolving D-loop and an adjacent intron. Our samples include populations of the continentally distributed species, A. tigrinum, plus all described species of Mexican ambystomatids. Sequence divergence is low, ranging from 0-8.5%, and most phylogenetic groupings are weakly supported statistically. We identified eight reasonably well-defined clades from the United States and Mexico, with the geographically isolated A. californiense from California as the probable sister group to the remaining taxa. Our sequence data are not capable of resolving the relationships among these clades, although the pattern of transitional-site evolution suggests that these eight lineages diverged during a period of rapid cladogenesis. We roughly calibrate a molecular clock and identify a few lineages that significantly deviate from the slow, baseline rate of 0.5-0.75% per million years. Our data also suggest that species boundaries for several U.S. and Mexican species need to be altered and that the concept of a continentally distributed, polytypic tiger salamander is not valid.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Expansions of population size leave characteristic signatures in mitochondrial "mismatch distributions." Consequently, these distributions can inform us about the history of changes in population size. Here, I study a simple model of population history that assumes that, t generations before the present, a population grows (or shrinks) suddenly from female size N0 to female size N1 . Although this model is simple, it often provides an accurate description of data generated by complex population histories. I develop statistical methods that estimate θ0 = 2uN0 , θ1 = 2uN1 , and τ = 2ut (where u is the mutation rate), and place a confidence region around these estimates. These estimators are well behaved, and insensitive to simplifying assumptions. Finally, I apply these methods to published mitochondrial data, and infer that a major expansion of the human population occurred during the late Pleistocene.
Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
For the haploid genetic model of Moran, the joint distribution of the numbers of distinct ancestors of a collection of nested subsamples is derived. These results are shown to apply to the diffusion approximations of a wide variety of other genetic models, including the Wright–Fisher process. The results allow us to relate the ancestries of populations sampled at different times. Analogous results for a line-of-descent process that incorporates the effect of mutation are given. Some results about the ages of alleles in an infinite-alleles model are described.
The Cordilleran Ice Sheet covered most of the Rocky Mountains west of the Continental Divide during each major Quaternary glacial advance. It extended southward onto the Columbia Plateau only west of Grand Coulee. In western Montana, one pre-Bull Lake glaciation, two stades of Bull Lake Glaciation, three stades of Pinedale Glaciation, and two stades of cirque Neoglaciation are known. In eastern Washington, one stade of Bull Lake Glaciation, two stades of Pinedale Glaciation, and cirque Neoglaciation are recognized. Major recessions separated stades of Bull Lake Glaciation; minor recessions separated stades of Pinedale Glaciation. The ice sheet blocked the Clark Fork River at Lake Pend Oreille at least five times, impounding Glacial Lake Missoula ; and it blocked the Columbia River at Grand Coulee at least three times, impounding Glacial Lake Columbia. During Bull Lake Glaciation the ice also blocked the Spokane Riverat Coeur d'Alene, impounding Glacial Lake Coeur d'Alene, and at Long Lake, impounding Glacial Lake Spokane. The ice dam impounding Glacial Lake Missoula collapsed at least three times, releasing catastrophic floods of enormous magnitude across the Columbia Plateau: once before and once during Bull Lake Glaciation, and once just after the early Pinedale glacial maximum. Loess accumulated on the plateau during each glaciation. At least seven different Pleistocene loesses and a Recent loess are recognized: two are of pre-Bull Lake age ; at least three, which comprise the Palouse Formation, are of Bull Lake age; two or more are of Pinedale age; and one is of Recent origin.
During the Fraser (Late Wisconsin) Glaciation, the Cordilleran ice sheet advanced southward from source areas in British Columbia and terminated in the United States between the Pacific Ocean and the Continental Divide. The ice sheet extended farthest along major south-trending valleys and lowlands that traverse the international boundary; it formed several composite lobes segregated by highlands and mountain ranges. Each lobe dammed sizable lakes that drained generally southward or westward along ice margins and across divides. Field evidence warrants considerable revision of the ice margin in northern Idaho and northeastern Washington. -from Authors
We present a phylogenetic analysis of the Ambystoma tigrinum complex, based on approximately 840 base pairs of mitochondrial-DNA sequence from the rapidly evolving D-loop and an adjacent intron. Our samples include populations of the continentally distributed species, A. tigrinum, plus all described species of Mexican ambystomatids. Sequence divergence is low, ranging from 0-8.5%, and most phylogenetic groupings are weakly supported statistically We identified eight reasonably well-defined clades from the United States and Mexico, with the geographically isolated A. californiense from California as the probable sister group to the remaining taxa. Our sequence data are not capable of resolving the relationships among these clades, although the pattern of transitional-site evolution suggests that these eight lineages diverged during a period of rapid cladogenesis. We roughly calibrate a molecular clock and identify a few lineages that significantly deviate from the slow, baseline rate of 0.5-0.75% per million years. Our data also suggest that species boundaries for several U.S. and Mexican species need to be altered and that the concept of a continentally distributed, polytypic tiger salamander is not valid.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
The origins of the present vascular flora of eastern Washington and northern Idaho have been traced from the early Cenozoic era to the present by means of published fossil floras, supplemented by interpretations of modern species' ranges. The flora is shown to be polyphyletic, resulting from three major immigrations coming from different sources at different times. Along a vegetation transect from steppe to subalpine forest, the contribution of these three floristic elements to the series of modern plant associations is expressed quantitatively, showing that each association contains species from at least two of the three elements.
For the haploid genetic model of Moran, the joint distribution of the numbers of distinct ancestors of a collection of nested subsamples is derived. These results are shown to apply to the diffusion approximations of a wide variety of other genetic models, including the Wright-Fisher process. The results allow us to relate the ancestries of populations sampled at different times. Analogous results for a line-of-descent process that incorporates the effect of mutation are given. Some results about the ages of alleles in an infinite-alleles model are described.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates.
We analyze the contribution of ancestral population size (θ) to T and the effect of uncertainty in θ on estimates of population divergence (τ) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on τ decrease when the range over which ancestral population size θ is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time.
There is a long-standing debate over whether or not the Pleistocene glaciations promoted speciation. While some models predict that extensive mixing of populations during interglacial expansion would have inhibited divergence, others postulate that divergence among allopatric glacial refuges or founder events during recolonization of previously glaciated areas would have promoted differentiation. Using a combination of traditional and coalescent based population genetic approaches, this study finds that the glaciations did not inhibit divergence among populations of the grasshopper Melanoplus oregonensis. Instead, drift associated with recolonization of previously glaciated areas, as well as divergence among multiple allopatric glacial refugia, have both contributed to differentiation in this montane grasshopper from the ‘sky islands’ of the northern Rocky Mountains. Significant population structure was detected by phylogenetic and FST analyses, including significant FST values among individual pairs of sky-island populations. In addition to clustering of haplotypes within populations, there is some evidence of regional phylogeographic structure, although none of the ‘regional groups’ form a monophyletic clade and there is a lack of concordance between the genealogical and geographical positions of some haplotypes. However, coalescent simulations confirm there is significant regional phylogeographic structure that most likely reflects divergence among multiple ancestral refugial populations, and indicate that it is very unlikely that the observed gene tree could have been produced by the fragmentation of a single widespread ancestral population. Thus, rather than inhibiting differentiation, the glaciations appear to have promoted population divergence in M. oregonensis, suggesting that they may have contributed to the radiation of Melanoplus species during the Pleistocene.
This study investigates the possibility that gene flow underlies the apparently maladaptive behavior of a riparian woodland population of the desert spider Agelenopsis aperta with respect to territorial, foraging, and antipredatory behaviors. I found that other local populations of A. aperta in the vicinity of the riparian woodland habitat are prey-limited and exhibit an aridlands phenotype (high aggressiveness in competitive interactions over energy-based territories and a lack of discrimination among potential prey types). The riparian woodland population deviates from surrounding populations in the area in that prey are abundant and this population shows a mixture of aridlands and riparian (low aggressiveness towards conspecifics and discrimination of prey profitability) phenotypes. Electrophoretic analyses of population subdivision in the area indicate that significant levels of gene flow have occurred, at least, sometime in the past. Drift fence analyses of spider movement futher indicate that there is marked unidirectional movement of spiders each year from the more arid habitats into the riparian woodland. Experimental manipulation of gene flow and predation pressure demonstrates that gene flow restricts adaptation in this habitat: one generation of predation pressure in the absence of gene flow is sufficient to cause a marked shift in spider behavior towards the expected riparian phenotype.
The role that inbreeding and coancestry play in the distribution of neutral genes is incorporated into the variance of a linear function to provide a simple cumulative expression of the variance among mean gene frequencies of groups of individuals. The total variance of gene frequencies is subdivided into components corresponding to genes within individuals, among individuals within groups, and among groups. Various intraclass correlations, some of which may be negative, of gene frequencies are formulated. The various types of parameters are considered for and extended to include further structuring of the population, separate sexes, systems of mating, and effective numbers. Estimators and tests of hypotheses for the parameters are developed.
Expansions of population size leave characteristic signatures in mitochondrial "mismatch distributions." Consequently, these distributions can inform us about the history of changes in population size. Here, I study a simple model of population history that assumes that, t generations before the present, a population grows (or shrinks) suddenly from female size N0 to female size N1. Although this model is simple, it often provides an accurate description of data generated by complex population histories. I develop statistical methods that estimate θ0 = 2uN0, θ1 = 2uN1, and τ = 2ut (where u is the mutation rate), and place a confidence region around these estimates. These estimators are well behaved, and insensitive to simplifying assumptions. Finally, I apply these methods to published mitochondrial data, and infer that a major expansion of the human population occurred during the late Pleistocene.
The discovery that orbital variations are the driving force behind Quaternary climate change provides an impetus to set local and regional records of environmental change into the global context, a principle that has been strongly embraced by Quaternary scientists working in New Zealand. Their major achievements and significant current initiatives are reviewed here. The importance of the New Zealand Quaternary stems from its geographical context: a climatically sensitive, remote oceanic, southern location spanning 17 degrees of the mid-latitudes; an obliquely convergent plate boundary setting resulting in a high mountain range athwart the prevailing westerlies, active volcanism, a youthful and dynamic landscape, and mountains high enough to maintain glaciers today; and a remarkably short prehistory. The resultant records show marked environmental changes due not only to climatic oscillations but also to vigorous, active tectonism and volcanism. The Taupo Volcanic Zone, containing the world's strongest concentration of youthful rhyolitic volcanoes, has produced at least 10 000 km3 of magma in the last 2 Ma. Climatic interpretations of records from marine sediments in the New Zealand region, together with several long sequences of alternating marine and terrestrial sediments, indicate broad synchrony with Northern Hemisphere events (within limitations of dating), although there are differences in detail for shorter-term climatic events. It is not yet certain that glacial advances coincided precisely with those in the Northern Hemisphere or were of similar duration. Late Cainozoic glaciation commenced c. 2.6-2.4 Ma but the record of glacial deposits is fragmentary and poorly dated except for the most recent events. The Last (Otira) Glaciation, from c. 100-10 ka, was characterized by at least five glacial advances including during the Last Glacial Maximum from 25 to 15 ka, when snowlines fell by 600-800 m. New Zealand evidence for cooling during the Younger Dryas stade is equivocal whilst isotopic records from speleothems, and other data, indicate warmer and wetter conditions from 10-7 ka, broadly conforming with records from mid-latitude Northern Hemisphere locations. Future advances will require sampling at shorter timescales, improvements in the accuracy and precision of existing dating methods and the development of new ones, extension of palaeoecological techniques to cover the full potential of New Zealand's diverse biota, and a stronger emphasis on quantification of palaeoclimatic parameters.
Exact and approximate expressions are obtained for the probability that the most frequent allele is oldest, in neutral allele models in which all mutations produce new alleles. The higher the mutation rate, the less likely is it that the most frequent allele would be oldest. The results are in agreement with simulation studies by Ewens and Gillespie (1974) (Theor. Popul. Biol.6, 35–57), and limit the range of validity of a suggestion made by Crow (1972) (J. Hered.63, 306–316) with respect to the statistical testing of the neutral allele hypothesis.
The expected number of segregating sites and the expectation of the average number of nucleotide differences among DNA sequences randomly sampled from a population, which is not in equilibrium, have been developed. The results obtained indicate that, in the case where the population size has changed drastically, the number of segregating sites is influenced by the size of the current population more strongly than is the average number of nucleotide differences, while the average number of nucleotide differences is affected by the size of the original population more severely than is the number of segregating sites. The results also indicate that the average number of nucleotide differences is affected by a population bottleneck more strongly than is the number of segregating sites.