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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.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Understanding how distributions of species change through time allows evaluation of hypotheses about factors shaping biogeographic patterns and evolutionary trajectories of genetic lineages. Ideally, such studies would assess whether population genetic processes are associated with geographic distribution shifts, loss or gain of distributional area through time, or fragmentation of distributional areas, information that can now be derived via ecological niche modeling. We examined the distributional changes through time in lineages and populations of Brown Creeper (Certhia americana), a widespread North American bird, to test biogeographic and population genetic hypotheses. In two populations with genetic support for population bottlenecks, Monterey County in California and the Sierra Madre Oriental in Mexico, ecological niche models indicated range contractions and increased fragmentation since the Last Glacial Maximum (LGM). Projections of niche models to the future suggested continuation of range contractions and fragmentation. Of the 3 major allopatric lineages of Brown Creeper (eastern North America, western North America, and southern North America and Central America), the most stable through time was the southern lineage, which corresponds with increased genetic diversity. The potential geographic distribution of the western lineage has remained stable in size but not location since the LGM, corresponding with a genetic signal of isolation by distance. The eastern lineage experienced range contractions during the LGM, likely resulting in the contemporary lack of genetic structure within the lineage. Finally, there is limited evidence of potential range overlap during the LGM between the western lineage and the other 2 lineages, although the overlap is limited to the Arizona sky islands between the west and south lineages. These results suggest that ecological niche modeling and population genetic data may be used as mutual predictors when investigating phylogeographic patterns and processes.
The Mexican Sheartail (Doricha eliza), an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.
Significant information is available regarding glacial history, lake level and vegetation history from several basins and volcanoes during the late Pleistocene in the Transmexican Volcanic Belt (TMVB). Here we present a synthesis and compilation of that information to establish the climatic conditions in this region during the Last Glacial Maximum. The data is organized in four time windows: Early Glacial: 2500022000 cal BP, Last Glacial Maximum: 2200018000 cal BP, Late Glacial: 1800015000 cal BP and Terminal Glacial 1500012000 cal BP. The late Pleistocene geomorphological evidence from Iztaccihuatl volcano offer the most complete record of glacial advances during the last 30000 yr; at other elevations the glacial history is fragmentary (due to volcanic activity) or more limited (due to lower altitudes). For the Early Glacial no evidence of glacial advance is recorded but data from the lacustrine basins indicate low lake levels. During the Last Glacial Maximum a decrease in temperature of 6 to 8° C is estimated, and the equilibrium line altitude is reconstructed at 3940 m for Iztaccíhuatl, 3400 m for Tancítaro,and 3650 m for Cofre de Perote. A downward displacement of ~ 1000 m for the limit of Pine forests with alpine vegetation, as well as changes in vegetation composition and distribution, are documented for the Late Glacial Maximum on the basis of palynological data. During this period low lake levels are recorded in the lakes of the Mexico and Lerma basins, while in the western sector of the TMVB most of the basins show low lake levels (Zirahuen, Zacapu and Cuitzeo) and only the record of Lake Patzcuaro suggests high stands for this period. Based on the synthesis of the data, a humidity gradient from the coasts towards the interior of the TMVB is inferred. For the Late Glacial period, a glacier retreat of ~100 m compared to the Last Glacial Maximum is detected at Iztaccíhuatl volcano. At the beginning of the Terminal Glacial all the glaciers retreated slowly and intermittently, then markedly after 14000 cal BP. At several lakes such as Tecocomulco, Texcoco, Cuitzeo and Zacapu sedimentation hiatus are recorded, indicating drier conditions.
We investigate the genetic variation between populations of the American sweetgum (Liquidambar styraciflua), a tree species with a disjunct distribution between northeastern Texas and Mexico, by analyzing sequences of two chloroplast DNA plastid regions in Mesoamerica. Our results revealed phylogeographical structure, with private haplotypes distributed in unique environmental space at either side of the Trans-Mexican Volcanic Belt, and a split in the absence of gene flow dating back ca. 4.2-1.4 million years ago (MYA). Species distribution modeling results fit a model of refugia along the Gulf and Atlantic coasts but the present ranges of US and Mesoamerican populations persisted disjunct during glacial/interglacial cycles. Divergence between the US and Mesoamerican (ca. 8.4-2.8 MYA) populations of L. styraciflua and asymmetrical gene flow patterns support the hypothesis of a long-distance dispersal during the Pliocene, with fragmentation since the most recent glacial advance (120,000 years BP) according to coalescent simulations and high effective migration rates from Mesoamerica to the USA and close to zero in the opposite direction. Our findings implicate the Trans-Mexican Volcanic Belt as a porous barrier driving genetic divergence of L. styraciflua, corresponding with environmental niche differences, during the Pliocene to Quaternary volcanic arc episode 3.6 MYA, and a Mesoamerican origin of populations in the USA.
The ocean thermohaline circulation is important for transports of heat and the carbon cycle. We present results from PMIP2 coupled atmosphere-ocean simulations with four climate models that are also being used for future assessments. These models give very different glacial thermohaline circulations even with comparable circulations for present. An integrated approach using results from these simulations for Last Glacial Maximum (LGM) with proxies of the state of the glacial surface and deep Atlantic supports the interpretation from nutrient tracers that the boundary between North Atlantic Deep Water and Antarctic Bottom Water was much shallower during this period. There is less constraint from this integrated reconstruction regarding the strength of the LGM North Atlantic overturning circulation, although together they suggest that it was neither appreciably stronger nor weaker than modern. Two model simulations identify a role for sea ice in both hemispheres in driving the ocean response to glacial forcing.
The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contrasting evidence regarding the changes in precipitation during this period. Some regions remained fairly moist and others had a significantly reduced precipitation. Many paleoecological records within the same region show apparently conflicting evidence on precipitation and forest stability. From these data, we propose and outline two demographic/genetic scenarios for cloud forests species based on opposite precipitation regimes: the dry refugia and the moist forests hypotheses. We searched for studies dealing with the population genetic structure of cloud forest and other montane taxa and compared their results with the proposed models. To date, the few available molecular studies show insufficient genetic evidence on the predominance of glacial aridity in the Neotropics. In order to disentangle the climatic history of the Neotropics, the present study calls for a general multi-disciplinary approach to conduct future phylogeographic studies. Given the contradictory paleoecological information, population genetic data on Neotropical cloud forest species should be used to explicitly test the genetic consequences of competing paleoecological models.
Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests-among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.
Phenological advancements driven by climate change are especially pronounced at higher latitudes, so that migrants from lower latitudes may increasingly arrive at breeding grounds after the appearance of seasonal resources. To explore this possibility, we compared dates of first arrival of Broad-tailed Hummingbirds (Selasphorus platycercus) to dates of flowering of plants they visit for nectar. Near the southern limit of the breeding range, neither hummingbird arrival nor first flowering dates have changed significantly over the past few decades. At a nearby migration stopover site, first flowering of a major food plant has advanced, but peak flowering has not. Near the northern limit of the breeding range, first and peak flowering of early-season food plants have shifted to earlier dates, resulting in a shorter interval between appearance of first hummingbirds and first flowers. If phenological shifts continue at current rates, hummingbirds will eventually arrive at northern breeding grounds after flowering begins, which could reduce their nesting success. These results support the prediction that migratory species may experience the greatest phenological mismatches at the poleward limits of their migration. A novel hypothesis based on these results posits that the poleward limit for some species may contract toward lower latitudes under continued warming.
Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter- and intraspecific diversification.
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.
We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950-2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and cross validation. Elevation bias tended to be negative (stations lower than expected) at high latitudes but positive in the tropics. Uncertainty is highest in mountainous and in poorly sampled areas. Data partitioning showed high uncertainty of the surfaces on isolated islands, e.g. in the Pacific. Aggregating the elevation and climate data to 10 arc min resolution showed an enormous variation within grid cells, illustrating the value of high-resolution surfaces. A comparison with an existing data set at 10 arc min resolution showed overall agreement, but with significant variation in some regions. A comparison with two high-resolution data sets for the United States also identified areas with large local differences, particularly in mountainous areas. Compared to previous global climatologies, ours has the following advantages: the data are at a higher spatial resolution (400 times greater or more); more weather station records were used; improved elevation data were used; and more information about spatial patterns of uncertainty in the data is available. Owing to the overall low density of available climate stations, our surfaces do not capture of all variation that may occur at a resolution of 1 km, particularly of precipitation in mountainous areas. In future work, such variation might be captured through knowledge-based methods and inclusion of additional co-variates, particularly layers obtained through remote sensing.
Aim We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad-scale historical events that have shaped the evolutionary history of Middle American highland taxa, and to test previous hypotheses of Neotropical speciation.
Location Middle America (Central America and Mexico).
Methods We used 2306 base pairs of mitochondrial gene sequences from 178 individuals to estimate the phylogeny and divergence times of New World pitviper lineages, focusing on three genera (Atropoides, Bothriechis and Cerrophidion) that are broadly co-distributed across Middle American highlands.
Results We found strong correspondence across three highland lineages for temporally and geographically coincident divergences in the Miocene and Pliocene, and further identified widespread within-species divergences across multiple lineages that occurred in the early–middle Pleistocene.
Main conclusions Available data suggest that there were at least three major historical events in Middle America that had broad impacts on species divergence and lineage diversification among highland taxa. In addition, we find widespread within-species genetic structure that may be attributable to the climatic changes that affected gene flow among highland taxa during the middle–late Pleistocene.
Large-scale geographical patterns of biotic specialization and the underlying drivers are poorly understood, but it is widely believed that climate plays an important role in determining specialization. As climate-driven range dynamics should diminish local adaptations and favor generalization, one hypothesis is that contemporary biotic specialization is determined by the degree of past climatic instability, primarily Quaternary climate-change velocity. Other prominent hypotheses predict that either contemporary climate or species richness affect biotic specialization. To gain insight into geographical patterns of contemporary biotic specialization and its drivers, we use network analysis to determine the degree of specialization in plant-hummingbird mutualistic networks sampled at 31 localities, spanning a wide range of climate regimes across the Americas. We found greater biotic specialization at lower latitudes, with latitude explaining 20-22% of the spatial variation in plant-hummingbird specialization. Potential drivers of specialization--contemporary climate, Quaternary climate-change velocity, and species richness--had superior explanatory power, together explaining 53-64% of the variation in specialization. Notably, our data provides empirical evidence for the hypothesized roles of species richness, contemporary precipitation and Quaternary climate-change velocity as key predictors of biotic specialization, whereas contemporary temperature and seasonality seem unimportant in determining specialization. These results suggest that both ecological and evolutionary processes at Quaternary time scales can be important in driving large-scale geographical patterns of contemporary biotic specialization, at least for co-evolved systems such as plant-hummingbird networks.
The effects of climate change on biodiversity should depend in part on climate displacement rate (climate-change velocity) and its interaction with species' capacity to migrate. We estimated Late Quaternary glacial-interglacial climate-change velocity by integrating macroclimatic shifts since the Last Glacial Maximum with topoclimatic gradients. Globally, areas with high velocities were associated with marked absences of small-ranged amphibians, mammals, and birds. The association between endemism and velocity was weakest in the highly vagile birds and strongest in the weakly dispersing amphibians, linking dispersal ability to extinction risk due to climate change. High velocity was also associated with low endemism at regional scales, especially in wet and aseasonal regions. Overall, we show that low-velocity areas are essential refuges for Earth's many small-ranged species.
Synopsis In 1967 Daniel Janzen published an influential paper titled "Why Mountain Passes Are Higher in the Tropics." Janzen derived a simple climatic-physiological model predicting that tropical mountain passes would be more effective barriers to organismal dispersal than would temperate-zone passes of equivalent altitude. This prediction derived from a recognition that the annual variation in ambient temperature at any site is relatively low in the tropics. Such low variation within sites not only reduces the seasonal overlap in thermal regimes between low- and high-altitude sites, but should also select for organisms with narrow physiological tolerances to temperature. As a result, Janzen predicted that tropical lowland organisms are more likely to encounter a mountain pass as a physiological barrier to dispersal (hence "higher"), which should in turn favor smaller distributions and an increase in species turnover along altitudinal gradients. This synthetic hypothesis has long been at the center of discussions of latitudinal patterns of physiological adaptation and of species diversity. Here we review some of the key assumptions and predictions of Janzen's hypothesis. We find general support for many assumptions and predictions, but call attention to several issues that somewhat ameliorate the generality of Janzen's classic hypothesis.
Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis.
Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America.
We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.
Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica.
Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma), and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected.
Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the Isthmus of Tehuantepec and more recent Pleistocene climatic events in driving isolation and population divergence. Coalescent analyses of the evolution of phenotypic traits suggest that selection is driving song evolution in wedge-tailed sabrewings but drift could not be rejected as a possibility for morphological divergence.
Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi-locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene. Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow-range taxa because of their resilience to past climate change.
Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N(e)) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N(e) using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr(-1) places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.
In the future, Arctic warming and the melting of polar glaciers will be considerable, but the magnitude of both is uncertain. We used a global climate model, a dynamic ice sheet model, and paleoclimatic data to evaluate Northern Hemisphere high-latitude warming and its impact on Arctic icefields during the Last Interglaciation. Our simulated climate matches paleoclimatic observations of past warming, and the combination of physically based climate and ice-sheet modeling with icecore constraints indicate that the Greenland Ice Sheet and other circum-Arctic ice fields likely contributed 2.2 to 3.4 meters of sea-level rise during the Last Interglaciation.
Abstract The Community Climate System Model version 3 (CCSM3) has recently 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 ...
AimWe tested whether populations of violet-crowned and green-fronted hummingbirds, Amazilia violiceps and Amazilia viridifrons, are genetically and environmentally differentiated, and examined the role of past geological and climatic changes in driving their diversification.LocationTrans-Mexican Volcanic Belt.Methods
Mitochondrial and nuclear DNA of individuals collected throughout the species' ranges were sequenced and then analysed using maximum-likelihood and Bayesian approaches. Species tree analysis, Bayesian species delimitation, divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of the Amazilia species, and the isolation-with-migration coalescent model was assessed to determine whether genetic divergence between Amazilia species occurred in the presence of gene flow.ResultsGenetic divergence between A. violiceps and A. viridifrons was shallow, with incomplete lineage sorting and introgression. Species delimitation supported three independent lineages: A. violiceps populations located north of the Trans-Mexican Volcanic Belt; a mixture of A. violiceps south of the volcanic belt and A. viridifrons populations; and A. villadai populations east of the Isthmus of Tehuantepec. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns support the model of species diversification by isolation with migration and habitat shifting in response to Pleistocene climatic fluctuations.Main conclusionsThe process of speciation in the Amazilia species complex may be explained by the combined effects of isolation resulting from the Trans-Mexican Volcanic Belt and the lowlands at the Isthmus of Tehuantepec and habitat shifting in response to Quaternary climatic changes.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
• 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.
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.