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Abstract

Large-scale phylogeographical patterns and the underlying factors driving species divergence in Mesoamerica are poorly understood, but it is widely documented that tectonic events and Pleistocene climate changes play an important role in determining species diversification. As glaciations in Mesoamerica developed only around high mountains, one hypothesis is that the known effects of the Last Glacial Maximum on the geographical distribution and genetic diversity of bird populations, producing the contraction/expansion latitudinal pattern observed in temperate bird species, should be largely undetected in resident bird populations inhabiting environmentally more stable habitats. To gain insight into the effects of Quaternary habitat and climate stability on the genetic diversity, we use ecological niche modelling and generalised linear modelling to determine the role of changes in habitat stability on the genetic diversity in eight widespread or range restricted hummingbird species. We found lesser changes in suitable habitat from past to present in most of the species than those predicted by palaeodistribution models at northern temperate regions. Contemporary seasonal precipitation, Quaternary habitat and climate stability had superior explanatory power, but the magnitude and directionality of their effects on genetic diversity varied between range-restricted and widely distributed species. We observed that the species studied have not responded equally to changes in climate stability in this complex region, suggesting that habitat differences and/or the altitudinal range of the hummingbird species influenced genetic diversity, and that the species-specific responses are not only linked to habitat stability in the region but also to contemporary seasonality associated with the availability of floral resources.

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How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of post-glacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site associated DNA (RAD) sequencing in two congeneric and co-distributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (D. merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear SNP private alleles and polymorphism. However, only D. deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D. deserti populations experienced a greater degree of loss than did D. merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.This article is protected by copyright. All rights reserved.
Book
The volume is broadly split into two main sections. The firsts consists of seven introductory chapters: biodiversity and priority setting; identifying endemic bird areas; global analyses; the prioritization of endemic brid areas; the conservation relevance of endemic bird areas; endemic bird areas as targets for conservation action; and regional introductions. The second, and larger part of the text looks at the endemic bird areas in detail. The section is split into six subsections, by region: North and Central America; Africa, Europe and the Middle East; continental Asia; SE Asian Islands, New Guinea and Australia; and the Pacific Islands. Within each regional subsection the endemic areas are detailed, providing information on : general characteristics; restricted-range species; threats and conservation; and location maps.
Article
AimWe studied which factors shape contemporary patterns of genetic structure, diversity and admixture in the canyon live oak (Quercus chrysolepis). Specifically, we tested two alternative hypotheses: (1) that areas with high habitat suitability and stability since the Last Glacial Maximum (LGM) sustain higher effective population sizes, resulting in increased levels of genetic diversity; and (2) that populations from areas with lower habitat stability show higher levels of genetic admixture due to their recurrent colonization by individuals originating from genetically differentiated populations. Furthermore, we analysed the relative importance of past and current habitat suitability and their additive effects on contemporary patterns of genetic structure.LocationCalifornia, USA.Methods We sampled 160 individuals from 33 localities across the distribution range of the canyon live oak in California and then combined information from 13 nuclear microsatellite DNA markers and climate niche modelling to study patterns of genetic variation in this species. We used Bayesian clustering analyses to analyse geographical patterns of genetic structure and admixture, and circuit theory to generate isolation-by-resistance (IBR) distance matrices.ResultsWe found that the degree of genetic admixture was higher in localities with lower inferred population stability, but that genetic diversity was not associated with habitat suitability or stability. Landscape genetic analyses identified habitat stability as the primary driver of population genetic differentiation.Main conclusionsThis study shows that habitat stability can be a major factor shaping genetic variation in wind-pollinated trees and supports the idea that stable regions contribute to genetic connectivity across different climatic periods. To our knowledge, this study is the first to report an association between patterns of genetic admixture and stability of local habitat.
Article
Aim. We investigated changes in distribution of cloud forests during the last 130 kyr, and tested whether these changes explain the spatial patterns of genetic diversity of the tree fern Alsophila firma (Cyatheaceae), a species restricted to this habitat. Location. Mexican cloud forests. Methods. We sampled 204 individuals from 16 localities. Genetic data consisted of DNA sequences for five chloroplast microsatellites and one nuclear gene. We used distribution modelling to predict the historical distribution of cloud forests during the last glacial period, using two palaeoclimate models: the Model for Interdisciplinary Research on Climate (MIROC) and the Community Climate System Model (CCSM). We tested the correlation between temporal cloud forest stability and genetic diversity and used an approximate Bayesian computation (ABC) framework to test two plausible demographic scenarios. Results. The range fluctuations observed for cloud forests during the last 130 kyr are key factors affecting the distribution of genetic variation in A. firma. Increased genetic diversity in areas with high temporal environmental suitability is probably the result of increased population sizes and higher interpopulation connectivity. In accordance with the expansion of cloud forests predicted by CCSM, the genetic data supported the scenario of a population expansion occurring c. 110 ka, followed by population divergence c. 20 ka. However, population dynamics involving expansion of suitable microclimates could reconcile the stability of cloud forests predicted by MIROC and the observed genetic patterns. Main conclusions. The predicted changes in the distribution of cloud forests were congruent with the population genetics of A. firma. However, the choice of palaeoclimate model has a substantial impact on the inferences drawn from the observed genetic and demographic patterns. The use of alternative palaeoclimate hypotheses and biome modelling can provide a common analytical framework for evaluating the historical cohesiveness of forest communities. This is the authors' post-print draft. The final version of the manuscript can be accessed through http://onlinelibrary.wiley.com/doi/10.1111/jbi.12396/full
Article
Recent empirical work on cloud forest-adapted species supports the role of both old divergences across major geographic areas and more recent divergences attributed to pleistocene climate changes. The shrub moussonia deppeana is distributed in northern mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographic history to infer the history of cloud forest in northern mesoamerica, and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the last glacial maximum. We found a deep evolutionary split in m. Deppeana about 6-3 ma, which could be consistent with a pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographic distribution, and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of m. Deppeana is not consistent with an expanding-contracting cloud forest archipelago model during the last glacial maximum. Instead, our data suggest that populations persisted across the geographic range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods. This article is protected by copyright. All rights reserved.
Article
China's Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3-0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.
Article
Aim: We test whether populations of the Mesoamerican azure-crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification. Location: Mexico. Methods: We sequenced the mitochondrial ATPase-6 and ATPase-8 genes and the control region of 130 individuals collected throughout the range of the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed. Results: The data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300—75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent-based test indicated that selection is driving the observed morphological differentiation. Main conclusions: Our findings implicate the Isthmus of Tehuantepec as a permeable barrier driving recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent-based test, suggest that selection has been strong enough to counteract the effects of gene flow.
Article
The cloud forests of Mesoamerica are highly endangered habitats and the existence of narrowly distributed cryptic endemics will increase the number of taxa at potential risk of extinction. Here, we investigate genetic divergence between populations of the azure-crowned hummingbird (Amazilia cyanocephala), a species complex of endemic hummingbirds to the montane forests of Mesoamerica, by analysing DNA sequences of four mitochondrial markers, morphological data and ecological niche modelling. Our results revealed the presence of two mtDNA lineages corresponding to subspecies A. c. cyanocephala distributed from Tamaulipas to Chiapas in Mexico and Amazilia c. guatemalensis distributed from southern Chiapas to Guatemala. The lineage split can be explained as a consequence of relative isolation of the populations in the different mountain ranges separated by the Motagua-Polochic-Jocotán fault system and corresponds to differences in morphology and to the lack of overlap in environmental space between subspecies. The divergence time estimates do not support the proposed model of a highly constrained temporal window at the end of the Pliocene as divergence at this barrier between cyanocephala and guatemalensis and splits of other bird taxa occurred during the Pleistocene.
Article
Unlike other migratory hummingbirds in North America, the broad-tailed hummingbird (Selasphorus platycercus) exhibits both long-distance migratory behaviour in the USA and sedentary behaviour in Mexico and Guatemala. We examined the evolution of migration linked to its northward expansion using a multi-perspective approach. We analysed variation in morphology, mitochondrial and nuclear DNA, estimated migration rates between migratory and sedentary populations, compared divergence times with the occurrence of Quaternary climate events, and constructed species distribution models to predict where migratory and sedentary populations resided during the Last Glacial Maximum (LGM) and Last Interglacial (LIG) events. Our results are consistent with a recent northward population expansion driven by migration from southern sedentary populations. Phylogeographical analyses and population genetics methods revealed that migratory populations in the USA and sedentary populations in Mexico of the platycercus subspecies form one admixed population, and that sedentary populations from southern Mexico and Guatemala (guatemalae) undertook independent evolutionary trajectories. Species distribution modelling revealed that the species is a niche tracker and that the climate conditions associated with modern obligate migrants in the USA were not present during the LIG, which provides indirect evidence for recent migratory behaviour in broad-tailed hummingbirds on the temporal scale of glacial cycles. The finding that platycercus hummingbirds form one genetic population and that suitable habitat for migratory populations was observed in eastern Mexico during the LIG also suggests that the conservation of overwintering sites is crucial for obligate migratory populations currently facing climate change effects. This article is protected by copyright. All rights reserved.
Article
Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessary to explain current patterns. We searched for concordant phylogeographic patterns and investigated their causes in three bird species (Momotus mexicanus, Melanerpes chrysogenys, and Passerina leclancherii) that belong to three different avian orders and are endemic to the northernmost range of the Neotropical dry forest. We obtained mitochondrial DNA (ND2 and COI or cyt b) and nuclear DNA (20454, GAPDH, MUSK, and TGFB) sequences for at least one locus from 162 individuals across all species and defined climatically stable areas using environmental niche model projections for the last 130,000 years to have a paleoenvironmental framework for the phylogeographic results. All three species showed marked phylogeographic structure, with breaks found in roughly similar areas, such as the border between the Mexican states of Guerrero and Oaxaca, and between southern Jalisco and Michoacán. Both of these regions are known biogeographic breaks among other taxa. Patterns of genetic diversity and differentiation were partially compatible with climatically stable areas. Coalescent analyses revealed recent population growth and estimated the deeper haplogroup divergence of all three taxa to have occurred within the last 600,000 years. The phylogeographic patterns found are noteworthy because they are maintained in a relatively small area for bird species with continuous ranges, and highlight a unique situation when compared to phylogeographic patterns found in other studies of Neotropical birds that have stressed the role of geographic barriers to explain intraspecific differentiation. Our results point to a scenario of population isolation resulting in the present phylogeographic structure, likely a result of historical climate fluctuations that have fragmented and reconnected the Neotropical dry forest. This study contributes to a growing body of evidence indicating active diversification of endemic lineages in the northern Neotropical dry forest region.
Article
Species diversity is largely underestimated by current taxonomy, precluding a precise understanding of evolutionary processes. Genetic data have increased our understanding of that cryptic diversity, and multilocus studies are now desirable. In this study, we used mitochondrial and nuclear DNA sequences to evaluate the taxonomic status of the western Mexico's populations of Phaethornis longirostris. We found differences of 4.2 % in mtDNA and different alleles for one nDNA locus between western and eastern Mexican populations. Molecular and morphological evidence support the separation of these populations (P. 1. mexicanus and P. 1. griseoventer) as the species Phaethornis mexicanus Hartert 1897. Phaethornis mexicanus is endemic to western Mexico and sister to the remaining populations of P. longirostris. The speciation of P mexicanus probably occurred around 880,000 years ago by a vicariant event involving climatic-vegetational changes.
Article
A new version of the Community Climate System Model (CCSM) has been developed and released to the climate community. CCSM3 is a coupled climate model with components representing the atmosphere, ocean, sea ice, and land surface connected by a flux coupler. CCSM3 is designed to produce realistic simulations over a wide range of spatial resolutions, enabling inexpensive simulations lasting several millennia or detailed studies of continental-scale climate change. This paper will show results from the configuration used for climate-change simulations with a T85 grid for atmosphere and land and a 1-degree grid for ocean and sea-ice. The new system incorporates several significant improvements in the scientific formulation. The enhancements in the model physics are designed to reduce or eliminate several systematic biases in the mean climate produced by previous editions of CCSM. These include new treatments of cloud processes, aerosol radiative forcing, land-atmosphere fluxes, ocean mixed-layer processes, and sea-ice dynamics. There are significant improvements in the sea-ice thickness, polar radiation budgets, equatorial sea-surface temperatures, ocean currents, cloud radiative effects, and ENSO teleconnections. CCSM3 can produce stable climate simulations of millenial duration without ad hoc adjustments to the fluxes exchanged among the component models. Nonetheless, there are still systematic biases in the ocean-atmosphere fluxes in western coastal regions, the spectrum of ENSO variability, the spatial distribution of precipitation in the Pacific and Indian Oceans, and the continental precipitation and surface air temperatures. We conclude with the prospects for extending CCSM to a more comprehensive model of the Earth's climate system.
Article
The montane insects of the Mexican Transition Zone form 2 well-defined groups: one occupies the ranges north of the Isthmus of Tehuantepec, the other the mountain systems south of the isthmus, the Sierra Madre de Chiapas and the mountains of Central America extending to the Nicaraguan depression. -from Author
Article
MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.
Article
Understanding how historical processes have either similarly, or differentially, shaped the evolution of lineages or biotic assemblages is important for a broad spectrum of fields. Gaining such understanding can be particularly challenging, however, especially for regions that have a complex geologic and biological history. In this study we apply a broad comparative approach to distill such regional biogeographic perspectives, by characterizing sets of divergence times for major biogeographic boundaries estimated from multiple codistributed lineages of snakes. We use a large combined (mitochondrial gene sequence) phylogeographic/phylogenetic dataset containing several clades of snakes that range across Middle America – the tropical region between Mexico and northwestern South America. This region is known for its complex tectonic history, and poorly understood historical biogeography. Based on our results, we highlight how phylogeographic transition zones between Middle and South America and the Nicaragua Depression appear to have undergone multiple episodes of diversification in different lineages. This is in contrast to other examples we find where apparently a single vicariant period is shared across multiple lineages. We specifically evaluate the distributions of divergence time estimates across multiple lineages and estimate the number of temporal periods of lineage diversification per biogeographic break. Overall, our results highlight a great deal of shared temporal divergence, and provide important hypotheses for yet unstudied lineages. These multi-lineage comparisons across multiple spatial and temporal scales provide excellent predictive power for identifying the roles of geology, climate, ecology and natural history in shaping regional biodiversity.
Article
The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopper Chorthippus parallelus is used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity - probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored using Chorthippus as a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.
Article
Sixty packrat middens were collected in Canyonlands and Grand Canyon National Parks, and these series include sites north of areas that produced previous detailed series from the Colorado Plateau. The exceptionally long time series obtained from each of three sites (> 48,000 14C yr BP to present) include some of the oldest middens yet discovered. Most middens contain a typical late-Wisconsinan glaciation mixture of mesic and xeric taxa, evidence that plant species responded to climate change by range adjustments of elevational distribution based on individual criteria. Differences in elevational range from today for trees and shrubs ranged from no apparent change to as much as 1200 m difference. The oldest middens from Canyonlands NP, however, differ in containing strictly xeric assemblages, including middens incorporating needles of Arizona single-leaf pinyon, far north of its current distribution. Similar-aged middens from the eastern end of Grand Canyon NP contain plants more typical of glacial climates, but also contain fossils of one-seed juniper near its current northern limit in Arizona. Holocene middens reveal the development of modern vegetation assemblages on the Colorado Plateau, recording departures of mesic taxa from low elevation sites, and the arrival of modern dominant components much later.
Article
A new packrat midden chronology from Playas Valley, southwestern New Mexico, is the first installment of an ongoing effort to reconstruct paleovegetation and paleoclimate in the U.S.A.–Mexico Borderlands. Playas Valley and neighboring basins supported pluvial lakes during full and/or late glacial times. Plant macrofossil and pollen assemblages from nine middens in the Playas Valley allow comparisons of two time intervals: 16,000–10,000 and 4000–0 14C yr B.P. Vegetation along pluvial lake margins consisted of open pinyon–juniper communities dominated by Pinus edulis, Juniperus scopulorum, Juniperus cf. coahuilensis, and a rich understory of C4 annuals and grasses. This summer-flowering understory is also characteristic of modern desert grassland in the Borderlands and indicates at least moderate summer precipitation. P. edulis and J. scopulorum disappeared or were rare in the midden record by 10,670 14C yr B.P. The late Holocene is marked by the arrival of Chihuahuan desert scrub elements and few departures as the vegetation gradually became modern in character. Larrea tridentata appears as late as 2190 14C yr B.P. based on macrofossils, but may have been present as early as 4095 14C yr B.P. based on pollen. Fouquieria splendens, one of the dominant desert species present at the site today, makes its first appearance only in the last millennium. The midden pollen assemblages are difficult to interpret; they lack modern analogs in surface pollen assemblages from stock tanks at different elevations in the Borderlands.
Article
• Poleward Pleistocene plant migration has been an important process structuring modern temperate and boreal plant communities, but the contribution of equatorward migration remains poorly understood. Paleobotanical evidence suggests Miocene or Pleistocene origin for temperate 'sky island' plant taxa in Mexico. These 'rear edge' populations situated in a biodiversity hotspot may be an important reserve of genetic diversity in changing climates. • We used mtDNA sequences, cpDNA sequences and chloroplast microsatellites to test hypotheses of Miocene vs Pleistocene colonization of temperate Douglas-fir in Mexico, explore geographic patterns of molecular variation in relation to Pleistocene climate history using ecological niche models, and assess the taxonomic and conservation implications. • We found strong evidence for Pleistocene divergence of Douglas-fir in Mexico (958 thousand yr before present (ka) with the 90% highest posterior density interval ranging from 1.6 million yr before present (Ma) to 491 ka), consistent with the southward Pleistocene migration hypothesis. Genetic diversity was high and strongly partitioned among populations. Spatial patterns of molecular variation and ecological niche models suggest a complex late Pleistocene history involving periods of isolation and expansion along mountain corridors. • These results highlight the importance of southward Pleistocene migration in establishing modern high-diversity plant communities and provide critical insights into proposals to conserve the unique biodiversity of Mexican Douglas-fir and associated taxa.
Article
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation in these jays coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's rule could account for some differences in timing estimates between mitochondrial DNA and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.