Phylogeographic insights into an irruptive pest outbreak

Irruptive forest insect pests cause considerable ecological and economic damage, and their outbreaks have been increasing in frequency and severity. We use a phylogeographic approach to understand the location and progression of an outbreak by the MPB (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that has caused unprecedented damage to lodgepole pine forests in western North America and is poised to expand its range across the boreal forest. We sampled MPB populations across British Columbia and Alberta and used phylogeographic methods to describe lineage diversification, characterize population structure, investigate expansion dynamics, and identify source populations of the outbreak. Using 1181 bp of mitochondrial DNA sequence from 267 individuals, we found high haplotype diversity, low nucleotide diversity, and limited lineage diversification. The overall pattern was consistent with isolation by distance at a continental scale, and with reduced diversity and population structure in the northerly, outbreak regions. Post-Pleistocene expansion was detected, however more recent expansion signals were not detected, potentially due to the size and rapid rate of range expansion. Based on the limited genetic structure, there were likely multiple source populations in southern British Columbia, although the magnitude of the demographic expansion and rate of spread have obscured the signature of these source populations. Our data highlight the need for caution in interpreting phylogeographic results for species with similar demographics.     

Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula

The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data.     

MATHEMATICS OF KIN‐ AND GROUP‐SELECTION: FORMALLY EQUIVALENT?

Evolutionary game theory is a general mathematical framework that describes the evolution of social traits. This framework forms the basis of many multilevel selection models and is also frequently used to model evolutionary dynamics on networks. Kin selection, which was initially restricted to describe social interactions between relatives, has also led to a broader mathematical approach, inclusive fitness, that can not only describe social evolution among relatives, but also in group structured populations or on social networks. It turns out that the underlying mathematics of game theory is fundamentally different from the approach of inclusive fitness. Thus, both approaches—evolutionary game theory and inclusive fitness—can be helpful to understand the evolution of social traits in group structured or spatially extended populations.     

Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii: testing historical and adaptive hypotheses

Combining phylogeographic and matrix correspondence approaches in the analysis of geographical variation provides a fruitful approach to inferring the causes of molecular and morphological evolution within species. Here we present a study on the gecko Tarentola delalandii on the island of Tenerife, Canary Islands, which provides an outstanding model of an exceptionally high degree of phylogeographic differentiation in magnitude and pattern on a small spatial scale. We reconstruct the population history of T. delalandii using phylogeographic information, matrix correspondence tests and estimates of divergence times in conjunction with geological data. It appears that populations differentiated on three precursor islands and secondary contact followed the junction of these islands. The cytochrome b sequence appears to be evolving at least at approximately 1% per million years in this species. Matrix correspondence tests indicate that morphological character systems may reflect ecological selection regimes (colour pattern), history (body dimensions) or both (scalation). The results imply that natural selection can override a historical legacy, but also underline the potential relevance of molecular phylogenetic data for the interpretation of geographical variation in morphology.     

Speciation durations and Pleistocene effects on vertebrate phylogeography.

An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic effects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspecific phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic differentiation among now-extant conspecific populations as well as in further sculpting pre-existing phylogeographic variety into many of today''s sister species; and (iii) for herpetofauna and fishes, inferred Pleistocene biogeographic influences on present-day taxa differ depending on alternative but currently plausible mtDNA rate calibrations.     

Lizards as model organisms for linking phylogeographic and speciation studies

Lizards have been model organisms for ecological and evolutionary studies from individual to community levels at multiple spatial and temporal scales. Here we highlight lizards as models for phylogeographic studies, review the published population genetics/phylogeography literature to summarize general patterns and trends and describe some studies that have contributed to conceptual advances. Our review includes 426 references and 452 case studies: this literature reflects a general trend of exponential growth associated with the theoretical and empirical expansions of the discipline. We describe recent lizard studies that have contributed to advances in understanding of several aspects of phylogeography, emphasize some linkages between phylogeography and speciation and suggest ways to expand phylogeographic studies to test alternative pattern‐based modes of speciation. Allopatric speciation patterns can be tested by phylogeographic approaches if these are designed to discriminate among four alternatives based on the role of selection in driving divergence between populations, including: (i) passive divergence by genetic drift; (ii) adaptive divergence by natural selection (niche conservatism or ecological speciation); and (iii) socially‐mediated speciation. Here we propose an expanded approach to compare patterns of variation in phylogeographic data sets that, when coupled with morphological and environmental data, can be used to to discriminate among these alternative speciation patterns. [Correction made after online publication (28/07/2010): (minor deletion in the last line of the abstract)].     

Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

Aim

Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction‐site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.

Location

Baja California and Southern California.

Methods

We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).

Results

Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern‐most portion of the range of C. ruber was not suitable habitat during the LGM.

Main conclusions

We provide the first explicitly model‐based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa.     

A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense,an endangered orchid with extremely small populations

Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, Dendrobium huoshanense, an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of D. huoshanense and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of D. huoshanense. The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of D. huoshanense have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of D. huoshanense. These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of D. huoshanense. According to our results, both two markers showed a high resolution for the phylogeographic studies of D. huoshanense. Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.     

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

Background  

Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs).     

Impact of ocean barriers, topography, and glaciation on the phylogeography of the catfish Trichomycterus areolatus (Teleostei: Trichomycteridae) in Chile

We examined the role of several earth history events on the phylogeographic distribution of the catfish Trichomycterus areolatus in Chile using the cytochrome b gene. We explored three biogeographic hypotheses: that sea level changes have resulted in the isolation of populations by drainages; that glaciation has impacted genetic diversity; and that ichthyological subprovince boundaries correspond to phylogeographic breaks in our focal species. We found seven well-supported clades within T. areolatus with high levels of genetic divergence. The strongest signal in our data was for an important role of sea level changes structuring populations. Five of the seven clades mapped cleanly to the geographic landscape and breaks corresponded closely to areas of narrowest continental shelf. In addition, few haplotypes were shared between rivers within clades, suggesting that only limited local movement of individuals has occurred. There was no relationship between the levels of genetic diversity and the proportion of individual drainages covered by glaciers during the last glacial maximum. Two phylogeographic breaks within T. areolatus did match the two previously identified faunal boundaries, but we found three additional breaks, which suggests that faunal breaks have only limited utility in explaining phylogeographic patterns. These results imply that the narrow continental shelf coupled with sea level changes had a strong influence on the obligate freshwater fishes in Chile.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 876–892.     

Drift effects on the multivariate floral phenotype of Calceolaria polyrhiza during a post‐glacial expansion in Patagonia

Quaternary environmental changes substantially impacted the landscape and promoted rapid evolutionary changes in many species; however, analyses of adaptive phenotypic variation in plants have usually neglected the underlying historical context. Here, we associate phylogeography and phenotypic evolution by analysing the divergence of Calceolaria polyrhiza multivariate floral phenotype after a Pleistocene post‐glacial expansion in Patagonia. Phenotypic matrix ( P ) properties (size, shape, orientation and phenotypic integration) of six refugium and six recent populations from two different phylogroups were compared following different approaches. We found that P ‐matrix shape and orientation remained stable despite the strong phylogeographic footprint of post‐glacial expansion. However, average proportional reductions in matrix size supported the expectation that drift had a significant effect on the floral phenotype in the northern phylogroup. When phylogeographic history was not included in the analyses, the results overestimated phenotypic differences, whereas under explicit phylogeographic control, drift appeared as the best explanation for matrix differences. In general, recent populations showed a larger phenotypic divergence among them, but a lower overall phenotypic variation than refugium populations. Random Skewers analyses indicated a lower potential response to selection in recently colonized populations than in refugium populations. We discuss that the combination of phylogeographic analyses with geographical distribution of functional phenotypic (genotypic) variation is critical not only to understand how historical effects influence adaptive evolution, but also to improve field comparisons in evolutionary ecology studies.     

The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of <Emphasis Type="Italic">Arcterica nana</Emphasis> (Maxim.) Makino (Ericaceae)

Previous phylogeographic studies of alpine plants in Japan have inferred that populations in central Honshu persisted during the Pleistocene climatic oscillations and suggested interglacial survival in high mountains. However, Arcterica nana (Maxim.) Makino (Ericaceae) exhibits a homogenous genetic structure throughout Japan and may therefore have a unique phylogeographic history. This inconsistency could have resulted from insufficient resolution of previously analyzed chloroplast DNA sequences. Therefore, we conducted a phylogeographic investigation based on amplified fragment length polymorphisms. Using 176 individuals from 21 populations, the relationships among individuals and populations were determined by principal coordinate analysis and a neighbor-joining tree, respectively. In addition, genetic differentiation was estimated using analysis of molecular variance and spatial autocorrelation analysis. These analyses demonstrate a homogenous structure throughout the entire Japanese range, supporting the previous cpDNA phylogeography. Although this genetic structure is inconsistent with those of other alpine plants, it is difficult to postulate that pre-existing genetic differentiation was swamped exclusively within A. nana. Therefore, this homogenous genetic structure may have been caused by the distinct history of populations of A. nana. Specifically, the southern-ward migration and the subsequent continuous populations enabled gene flow throughout the Japanese archipelago during the last glacial period. Thus, our data suggest that alpine plants in the Japanese archipelago did not always experience a shared distribution change following climatic oscillations.     

Historical biogeography of Drosophila simulans based on Y-chromosomal sequences

Y-chromosomal sequences have been used for phylogeographic studies in humans and other mammals, but so far have been ignored as a source of historical information in Drosophila and other insects with X/Y sex determination. Here, we present the first phylogeographic study of Drosophila simulans based on the Y chromosome. Geographic distribution of Y-chromosomal haplotypes suggests a high degree of population subdivision within Africa, as well as between the African and cosmopolitan groups of populations. Consistent with earlier studies based on autosomal and X-linked loci, our results suggest that D. simulans originated in Madagascar or East Africa, and that the South and West African populations of this species are derived.     

The coup de grace for the nested clade phylogeographic analysis?

Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has published a large fraction of the literature on the topic--both pro and con. A recent study by Panchal and Beaumont (2007) finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other all-encompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.     

The coup de grâce for the nested clade phylogeographic analysis?

Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has published a large fraction of the literature on the topic — both pro and con. A recent study by Panchal and Beaumont (2007) finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other all-encompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.     

Mechanisms of population differentiation in seabirds

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.     

Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci?

One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.     

Phylogeography and demography of sympatric sister surfperch species, Embiotoca jacksoni and E. lateralis along the California coast: historical versus ecological factors

With 18 closely related endemic species that radiated in a diversity of ecological niches, the California surfperches (Embiotocidae) species flock is a good candidate for the study of sympatric speciation. Resource partitioning has been suggested as an important driving force in the radiation of the surfperch family. Within the family, two congeneric sister species, Embiotoca jacksoni and E. lateralis, are known to compete strongly for a preferred single food resource and may be used as a model of ecological interactions for the family. Along the California coast, the distribution of the two species differs. Embiotoca jacksoni has a continuous range, whereas E. lateralis shows a disjunction with a distribution gap in the Southern California Bight. Two hypotheses may explain this disjunct distribution. Ecological competition may have displaced E. lateralis in favor of E. jacksoni. Alternatively, a common vicariant event may have separated the species into northern and southern populations, followed by secondary contact in E. jacksoni but not in E. lateralis. The two hypotheses predict different phylogeographic and demographic signatures. Using a combined phylogeographic and coalescent approach based on mitochondrial control region data, we show that vicariance can only account for a portion of the observed divergences. Our results are compatible with a significant role played by ecological competition in the southern range of the species.     

Mitochondrial Diversity and Phylogeographic Patterns of Gekko gecko(Squamata: Gekkonidae) in Thailand

The Tokay Gecko, Gekko gecko(Linnaeus, 1758) is widely distributed in Asia and there have been concerns regarding locally decreasing populations due to overexploitation for traditional Chinese medicine. Previous studies of the genetic relationships of G. gecko populations included few populations from Thailand. Here we investigated the phylogeographic patterns of G. gecko from different regions in Thailand using mitochondrial cytochrome b sequences. Phylogenetic analyses revealed two lineages: one(Lineage A) comprising populations from Laos, Vietnam, and Thailand; and a second(Lineage B) comprising three genetically distinct groups within Thailand alone. Some Thai populations were found to have both lineages represented within them. Highly significant genetic differentiation(FST) showed geographic population structuring in Lineage B, indicating limited gene flow among groups in Thailand. Although G. gecko has a wide distribution and is well adapted to human habitation, the observed genetic structure could potentially be explained by geographic barriers such as mountain ranges. In Lineage A, our study provided primary phylogeographic evidence for lineage mixture that might be a result of human-mediated transport. Future research should include more extensive sampling across the geographic distribution of G. gecko and a landscape genetics approach could be applied for conservation planning.