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Understanding how species have responded to past climate change may help refine projections of how species and biotic communities will respond to future change. Here, we integrate estimates of genome-wide genetic variation with demographic and niche modeling to investigate the historical biogeography of an important ecological engineer: the dusky-footed woodrat, Neotoma fuscipes. We use RADseq to generate a genome-wide dataset for 71 individuals from across the geographic distribution of the species in California. We estimate population structure using several model-based methods and infer the demographic history of regional populations using a site frequency spectrum-based approach. Additionally, we use ecological niche modeling to infer current and past (Last Glacial Maximum) environmental suitability across the species' distribution. Finally, we estimate the directionality and possible spatial origins of regional population expansions. Our analyses indicate this species is subdivided into three regionally distinct populations, with the deepest divergence occurring ~1.7 million years ago across the modern-day San Francisco-Bay Delta region; a common biogeographic barrier for the flora and fauna of California. Our models of environmental suitability through time coincide with our estimates of population expansion, with relative long-term stability in the southern portion of the range, and more recent expansion into the northern end of the range. Our study illustrates how the integration of genome-wide data with spatial and demographic modeling can reveal the timing and spatial extent of historic events that determine patterns of biotic diversity and may help predict biotic response to future change.

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis-based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis-specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.

Leporid remains are common in Quaternary fossil assemblages and are useful paleoenvironmental indicators. Identifying leporid fossils to species is challenging, though previous work has shown that identifications are more feasible if fossils can be narrowed down to a subset of potential species occurring across limited spatial scales. We sampled 120 adult and nine juvenile dentaries of six extant western North American species (Lepus americanus, L. californicus, L. townsendii, Sylvilagus audubonii, S. bachmani, and S. nuttallii) to establish useful characters for genus and species-level identification of late Quaternary leporid fossils in California. Most individuals can be differentiated from individuals of other species using a combination of lower third premolar enamel folding patterns and dental measurements. However, it is difficult to discriminate dental elements among L. californicus and L. townsendii and elements of S. nuttallii from S. audubonii, S. bachmani, and L. americanus. Here we present criteria for differentiating western leporid dental remains, apply the criteria to identify specimens recovered from several late Quaternary fossil deposits at Rancho La Brea (RLB), California, collectively known as Project 23, and reconstruct changes in relative fossil leporid abundances there. Using our criteria, we identified two extant species, S. audubonii and S. bachmani, among the Project 23 fossils. In addition to relative abundance changes across several RLB deposits, S. audubonii and S. bachmani generally become larger through time, possibly in response to local environmental changes. Establishing region-specific identification criteria as done here may prove useful for discerning morphologically similar species at prehistoric sites elsewhere.

The Indo-Pacific Pollen Database (IPPD) is the brainchild of the late Professor Geoffrey Hope, who gathered pollen records from across the region to ensure their preservation for future generations of palaeoecologists. This noble aim is now being fulfilled by integrating the IPPD into the online Neotoma Palaeoecology Database, making this compilation available for public use. Here we explore the database in depth and suggest directions for future research. The IPPD comprises 226 fossil pollen records, most postdating 20 ka, but some extending as far back as 50 ka or further. Over 80 % of the records are Australian, with a fairly even distribution between the different Australian geographical regions, the notable exception being Western Australia, which is only represented by 3 records. The records are also well distributed in modern climate space, the largest gap being in drier regions due to preservation issues. However, many of the records contain few samples or have fewer than 5 chronology control points, such as radiocarbon, luminescence or Pb-210 for the younger sequences. Average sedimentation rate for the whole database, counted as years per cm, is 64.8 yr/cm, with 61 % of the records having a rate of less than 50 yr/cm. The highest sedimentation rate by geographical region occurs on Australia's east coast, while the lowest rates are from the Western Pacific. Overall, Australia has a higher sedimentation rate than the rest of the Indo-Pacific region. The IPPD offers many exciting research opportunities, such as examination of human impact on regional vegetation, contrasting first human arrival and colonisation, and assessment of rates of vegetation change during the Holocene. Merging the IPPD into Neotoma also facilitates inclusion of data from the Indo-Pacific region into global syntheses. [ABSTRACT FROM AUTHOR]

The dusky-footed woodrat (Neotoma fuscipes) is an endemic North American rodent belonging to the family Cricetidae. We present here the first complete mitogenome within the Neotoma genus. The mitogenome is 16,199 bp in length, and has a structure and gene organization similar to other rodent species (e.g. Mus musculus, Peromyscus maniculatus and Microtus fortis calamorum). The overall base composition is A (35.2%), C (25.5%), G (12.3%), T (27.0%), with a GC content of 37.8%, similar to other rodents. This mitogenome serves as a foundation for future phylogenetic, phylogeographic and population genetic studies.

Increasingly, ecological modellers are integrating paleodata with future projections to understand climate-driven biodiversity dynamics from the past through the current century. Climate simulations from earth system models are necessary to this effort, but must be debiased and downscaled before they can be used by ecological models. Downscaling methods and observational baselines vary among researchers, which produces confounding biases among downscaled climate simulations. We present unified datasets of debiased and downscaled climate simulations for North America from 21 ka BP to 2100AD, at 0.5° spatial resolution. Temporal resolution is decadal averages of monthly data until 1950AD, average climates for 1950-2005 AD, and monthly data from 2010 to 2100AD, with decadal averages also provided. This downscaling includes two transient paleoclimatic simulations and 12 climate models for the IPCC AR5 (CMIP5) historical (1850-2005), RCP4.5, and RCP8.5 21st-century scenarios. Climate variables include primary variables and derived bioclimatic variables. These datasets provide a common set of climate simulations suitable for seamlessly modelling the effects of past and future climate change on species distributions and diversity.

Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North America for the past 21 000 years. Both SDMs and CLMs performed poorly when projected to time periods that are temporally distant and climatically dissimilar from those in which they were fit; however, CLMs generally outperformed SDMs in these instances, especially when models were fit with sparse calibration datasets. Additionally, CLMs did not over-fit training data, unlike SDMs. The expected emergence of novel climates presents a major forecasting challenge for all models, but CLMs may better rise to this challenge by borrowing information from co-occurring taxa.

Are we entering a new ‘Golden Age’ of biogeography, with continued development of infrastructure and ideas? We highlight recent developments, and the challenges and opportunities they bring, in light of the snapshot provided by the 7th biennial meeting of the International Biogeography Society (IBS 2015). We summarize themes in and across 15 symposia using narrative analysis and word clouds, which we complement with recent publication trends and ‘research fronts’. We find that biogeography is still strongly defined by core sub-disciplines that reflect its origins in botanical, zoological (particularly bird and mammal), and geographic (e.g., island, montane) studies of the 1800s. That core is being enriched by large datasets (e.g. of environmental variables, ‘omics’, species’ occurrences, traits) and new techniques (e.g., advances in genetics, remote sensing, modeling) that promote studies with increasing detail and at increasing scales; disciplinary breadth is being diversified (e.g., by developments in paleobiogeography and microbiology) and integrated through the transfer of approaches and sharing of theory (e.g., spatial modeling and phylogenetics in evolutionary–ecological contexts). Yet some subdisciplines remain on the fringe (e.g., marine biogeography, deep-time paleobiogeography), new horizons and new theory may be overshadowed by popular techniques (e.g., species distribution modelling), and hypotheses, data, and analyses may each be wanting. Trends in publication suggest a shift away from traditional biogeography journals to multidisciplinary or open access journals. Thus, there are currently many opportunities and challenges as biogeography increasingly addresses human impacts on, and stewardship of, the planet (e.g., Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services). As in the past, biogeographers doubtless will continue to be engaged by new data and methods in exploring the nexus between biology and geography for decades into the future. But golden ages come and go, and they need not touch every domain in a discipline nor affect subdisciplines at the same time; moreover, what appears to be a Golden Age may sometimes have an undesirable ‘Midas touch’. Contexts within and outwith biogeography—e.g., methods, knowledge, climate, biodiversity, politics—are continually changing, and at times it can be challenging to establish or maintain relevance. In so many races with the Red Queen, we suggest that biogeography will enjoy greatest success if we also increasingly engage with the epistemology of our discipline.

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a "missing middle": Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit.

Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change (1). Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance (2,3). However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size (4,5) and the spread of agriculture in North America (6,7). Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity., How are plant and animal communities organized, and does their structure change through time? This question has dominated many decades of research on community assembly rules and is critical to [...]

Communities have been shaped in numerous ways by past climatic change; this process continues today (1). At the end of the Pleistocene epoch about 11,700 years ago, North American communities were substantially altered by the interplay of two events. The climate shifted from the cold, arid Last Glacial Maximum to the warm, mesic Holocene interglacial, causing many mammal species to shift their geographic distributions substantially (2,3). Populations were further stressed as humans arrived on the continent (4). The resulting megafaunal extinction event, in which 70 of the roughly 220 largest mammals in North America (32%) became extinct (5), has received much attention. However, responses of small mammals to events at the end of the Pleistocene have been much less studied, despite the sensitivity of these animals to current and future environmental change. Here we examine community changes in small mammals in northern California during the last 'natural' global warming event at the Pleistocene-Holocene transition and show that even though no small mammals in the local community became extinct, species losses and gains, combined with changes in abundance, caused declines in both the evenness and richness of communities. Modern mammalian communities are thus depauperate not only as a result of megafaunal extinctions at the end of the Pleistocene but also because of diversity loss among small mammals. Our results suggest that across future landscapes there will be some unanticipated effects of global change on diversity: restructuring of small mammal communities, significant loss of richness, and perhaps the rising dominance of native 'weedy' species., Mammal communities that reassembled after the end-Pleistocene extinctions now face new threats of species extinction and reorganization because of similar events--intense human influence coupled with a rapidly warming climate. Understanding [...]

Author(s): S. Kathleen Lyons; Kathryn L. Amatangelo; Anna K. Behrensmeyer; Antoine Bercovici; Jessica L. Blois; Matt Davis; William A. DiMichele; Andrew Du; Jussi T. Eronen; J. Tyler Faith; Gary R. [...]

We used a comparative, multimarker approach to investigate the conservation genetics of an arboreal vole (the Sonoma tree vole [Arborimus pomo]) in the Pacific Northwest of North America. We compared geographic patterns and overall levels of genetic diversity based on 55 amplified fragment length polymorphism (AFLP) loci with those based on a single, commonly used mitochondrial locus, the control region. Although examination of the control region data revealed the presence of 2 distinct mitochondrial DNA (mtDNA) clades within A. pomo (1 in the north and 1 in the south of the species' range), the nuclear perspective provided by AFLP did not reveal a similar geographic division within the species, supporting instead that A. pomo consists of a single panmictic population. Genetic diversity estimates based on the mtDNA data (gene diversity = 0.79 and 0.80 for the 2 clades) were much greater than those based on AFLP (gene diversity = 0.31 and 0.19 for the 2 dades). These contrasting results reflect inherent differences between mitochondrial and nuclear loci in mutation rate, effective population size, expected time to monophyly, and mode of inheritance, and highlight the utility of using the combination of AFLP and mtDNA when assessing the genetic status of wild populations and species of mammals, especially those of conservation concern. In the case of A. pomo, our combined AFLP and mtDNA data support the recognition of the southern Sonoma tree voles as a distinct management unit within the species. Key words: amplified fragment length polymorphism (AFLP), Arborimus pomo, genetic diversity, mitochondrial DNA (mtDNA), Sonoma tree vole

Author(s): S. Kathleen Lyons (corresponding author) [1]; Joshua H. Miller [2]; Kathryn L. Amatange [3]; Anna K. Behrensmeyer [4]; Antoine Bercovici [1]; Jessica L. Blois [4]; Matt Davis [5]; William [...]