Development and field validation of a regional,management‐scale habitat model: A koala Phascolarctos cinereus case study

Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional‐scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently‐collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2‐km spatial filter and by modeling separately two subregions separated by the 500‐m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground‐truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground‐truth sites. Similarly, a site habitat quality index at ground‐truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site‐based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field‐validated models of similar resolution would assist in guiding management of conservation‐dependent species.     

Anthropogenic changes to the landscape resulted in colonization of koalas in north‐east New South Wales,Australia

Significant changes in the distribution and persistence of species have been driven by Pleistocene cyclical climate changes and, more recently, by human modification of the environment. In eastern Australia, Pleistocene cyclical patterns in temperature and aridity led to the expansion and retraction of rainforest and likely affected the distribution of the koala (Phascolarctos cinereus, family Phascolarctidae), a species preferring dry or open woodland. More recently, anthropogenic landscape modification has led to a large‐scale change in distribution of the koala following the destruction of approx. 75 000 ha of subtropical rainforest in north‐east New South Wales termed the ‘Big Scrub’. Sharing of the control region haplotypes to the north and south of this region indicate historical connectivity of coastal koala populations. However, the majority (110/115) of sampled koalas from this region shared a single mitochondrial control region haplotype, suggesting that koalas did not persist in multiple refugial pockets within a heterogenous rainforest but expanded into the region following deforestation. Bayesian cluster analysis of microsatellite data consistently identified two clusters of koalas. One cluster, in the north of the area, had high microsatellite diversity (10 alleles per locus, He = 0.79) and clustered with koalas further to the north, thus suggesting a southerly expansion into the cleared area. To the south was a cluster with significantly lower diversity (six alleles per locus, He = 0.59, P < 0.001). It is possible there has been restricted or filtered movement of koalas between these clusters, which coincides with a cleared river valley and associated roads or immigration from populations both to the north and to the south. This study gives an insight into the timescale of changes in species distribution following rapid alterations to suitable habitat.     

Modelling changes in the distribution of the critical food resources of a specialist folivore in response to climate change

Aim An important consideration when planning to conserve a species under climate change is to understand how the distribution of its food resources may also contract or shift under those same climatic conditions. Here, we use a case study to demonstrate a spatial conservation planning approach to inform decisions about where, under climate change, to protect and restore critical food and habitat resources for highly specialized species. Location Eastern Australia. Methods We developed fitted models for the koala (Phascolarctos cinereus) and five of its key eucalypt food trees using the maximum entropy algorithm available in Maxent. We then projected these models using a range of IPCC A1FI climate change scenarios and identified areas with a higher probability of occurrence. We calculated where the koala and its food trees may co‐occur under future climate change. Results The koala and its food trees experienced significant range contractions as climate change progressed, sometimes to regions outside their current distributions. The inland species Eucalyptus camaldulensis and Eucalyptus coolabah contracted from the more arid interior, which is outside the koala range, but persisted in the eastern regions of the koala’s range, while Eucalyptus viminalis, Eucalyptus populnea and Eucalyptus tereticornis contracted eastwards and southwards, with a fragmented distribution. The highest probabilities of overlap between koalas and their food trees were identified in fragmented coastal and southern regions of the koala’s current range. Main conclusions The application of a robust species distribution modelling decision support tool identified important changes, under climate change, in the distribution of a specialist species and its key food trees. These distributions did not change in complete synergy and therefore areas of overlap varied, depending on the food tree species modelled. This is of particular importance in a conservation planning context, when considering targeted protection and restoration of species‐specific habitat resources.     

Effects of Quaternary climatic fluctuations on the distribution of Neotropical savanna tree species

In order to develop niche models for tree species characteristic of the cerrado vegetation (woody savannas) of central South America, and to hindcast their distributions during the Last Glacial Maximum and Last Inter‐Glacial, we compiled a dataset of tree species checklists for typical cerrado vegetation (n = 282) and other geographically co‐occurring vegetation types, e.g. seasonally dry tropical forest (n = 355). We then performed an indicator species analysis to select ten species that best characterize typical cerrado vegetation and developed niche models for them using the Maxent algorithm. We used these models to assess the probability of occurrence of each species across South America at the following time slices: Current (0 ka pre‐industrial), Holocene (6 ka BP), Last Glacial Maximum (LGM – 21 ka BP), and Last Interglacial (LIG – 130 ka BP). The niche models were robust for all species and showed the highest probability of occurrence in the core area of the Cerrado Domain. The palaeomodels suggested changes in the distributions of cerrado tree species throughout the Quaternary, with expansion during the LIG into the adjacent Amazonian and Atlantic moist forests, as well as connections with other South American savannas. The LGM models suggested a retraction of cerrado vegetation to inter‐tableland depressions and slopes of the Central Brazilian Highlands. Contrary to previous hypotheses, such as the Pleistocene refuge theory, we found that the widest expansion of cerrado tree species seems to have occurred during the LIG, most probably due to its warmer climate. On the other hand, the postulated retractions during the LGM were likely related to both decreased precipitation and temperature. These results are congruent with palynological and phylogeographic studies in the Cerrado Domain.     

At what spatial scales does resource selection vary? A case study of koalas in a semi‐arid region

The conservation of any species requires understanding and predicting the distribution of its habitat and resource use, including the effects of scale‐dependent variation in habitat and resource quality. Consequently, testing for resource selection at the appropriate scales is critical. We investigated how the resource selection process varies across scales, using koalas in a semi‐arid landscape of eastern Australia as a case study. We asked: at what scales does tree selection by koalas vary across regions? We tested the importance of the variation of our ecological predictors at the following scales: (i) the site‐scale (a stand of trees representing an individual koala's perception of local habitat); (ii) the landscape‐scale (10 × 10 km area representing a space within which a population of koalas exists); and (iii) a combination of these scales. We used a mixed‐modelling approach to quantify variation in selection of individual trees by koalas among sites and landscapes within a 1600 km² study area. We found that tree species, and tree height, were the most important factors influencing tree selection, and that their effect did not vary across scales. In contrast, preferences for trees of different condition, which is the state of tree canopy health, did vary across landscapes, indicating spatial variation in the selection of trees with respect to tree condition at the landscape‐scale, but not at the site‐scale. We conclude that resource selection processes can depend on the quality of those resources at different scales and their heterogeneous nature across landscapes, highlighting the consequence of scale‐dependent ecological processes. Designing studies that capture the heterogeneity in habitat and resources used by species that have an extensive distribution is an important prerequisite for effective conservation planning and management.     

Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad‐tailed hummingbird (Selasphorus platycercus)

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 multiperspective 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.     

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate‐based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large‐scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.     

Pleistocene glaciation explains the disjunct distribution of the Chestnut‐vented Nuthatch (Aves,Sittidae)

Pleistocene climatic oscillations have played an important role in shaping many species’ current distributions. In recent years, there has been increasing interest in studying the effects of glacial periods on East Asian birds. Integrated approaches allow us to study past distribution range changes due to Pleistocene glaciation, and how these changes have affected current population genetic structure, especially for species with unusual distribution patterns. The Wuyi disjunction is the disjunct distribution of birds between the Wuyi Mountains in south‐eastern China and south‐western China. Although several species exhibit the Wuyi disjunction, the process behind this unusual distribution pattern has remained relatively unstudied. Therefore, we used the Chestnut‐vented Nuthatch Sitta nagaensis as a model species to investigate the possible causes of the Wuyi disjunction. Based on phylogenetic analyses with three mitochondrial and six nuclear regions, the Wuyi population of the Chestnut‐vented Nuthatch was closely related to populations in mid‐Sichuan, from which it diverged approximately 0.1 million years ago, despite the long geographical distance between them (over 1,300 km). In contrast, geographically close populations in mid‐ and southern Sichuan were genetically divergent from each other (more than half a million years). Ecological niche modelling suggested that the Chestnut‐vented Nuthatch has experienced dramatic range expansions from Last Interglacial period to Last Glacial Maximum, with some range retraction following the Last Glacial period. We propose that the Wuyi disjunction of the Chestnut‐vented Nuthatch was most likely due to recent range expansion from south‐western China during the glacial period, followed by postglacial range retraction.     

Evolutionary history of Apocheima cinerarius (Lepidoptera: Geometridae), a female flightless moth in northern China

The alterations in the phylogeographical structures of insects in response to the uplift of the Qinghai–Tibet Plateau and the Quaternary glaciations in eastern Asia, particularly in northern China, remain largely unknown. In this study, we selected Apocheima cinerarius, a moth with flightless females, using molecular data (complete mitochondrial genomes and nuclear data) and ecological niche modelling (ENM) to investigate the effects of paleoclimatic changes on the evolutionary history of insects in the area of northern China. The phylogenetic tree of complete mitochondrial genomes indicated that there were two lineages, the western and eastern lineages. The nuclear gene analyses also detected unique haplotypes in each lineage. Time of the most recent common ancestor (TMRCA) of the two lineages was approximately in Early–Middle Pleistocene. Bayesian skyline plots revealed that the western lineage underwent a population expansion event after the Last Glacial Maximum, whereas the eastern lineage underwent expansion between the Last Interglacial and the Last Glacial Maximum. Our results suggest that A. cinerarius expanded eastward from western sites until the moth was distributed across the entire region of northern China. Then, A. cinerarius underwent contraction into isolated glacial refugia followed by subsequent expansion driven by Pleistocene climate changes, which established a narrow sympatric area. Our results indicate that the Quaternary environmental fluctuations had profound influences on the diversification and demography of an insect in northern China, and the same species in north‐western China and north‐eastern China have different demographic histories.     

Vegetation cover of Brazil in the last 21 ka: New insights into the Amazonian refugia and Pleistocenic arc hypotheses

Aim

The two main hypotheses about the Neotropical palaeovegetation, namely that of Amazonian refugia by Haffer and of the Pleistocene arc by Prado and Gibbs, are still constantly debated. We offer new insights on this debate using ecological niche modelling with combined climate–soil predictors to test both hypotheses, reconstruct the palaeovegetation of the Last Glacial Maximum (LGM; 21 ka) and Mid‐Holocene (Mid‐H; 6 ka) and indicate the configuration of refugia areas.

Location

Brazil.

Time period

Last 21 ka.

Major taxa studied

Biomes.

Methods

We modelled the environmental space of the 10 most representative biomes with the RandomForest classifier, using climate predictors from three atmospheric general circulation models (CCSM4, MPI‐ESM‐P and MIROC‐ESM) and soil predictors, the same for the different situations. Based on the consensus among the models, we reconstructed the palaeovegetation cover for LGM and Mid‐H and used fossil pollen sites to validate the reconstructions in a direct comparison.

Results

The climate in the past was cooler and wetter throughout most of the territory. The Amazon basin region was the most affected by climate change in the last 21 ka, with equatorial rain forest retracting to refugia areas, while the tropical rain forest (with climatic preferences similar to the Atlantic forest) expanded in the basin. In southern Brazil, the mixed forest (Araucaria forest) shifted to lower latitudes, while the grasslands expanded. In most biomes, the greatest changes occurred in the ecotonal zones, supported by pollen fossils.

Main conclusions

With regard to Haffer's hypothesis, the forests of the Amazonian lowlands retreated to refugia areas, while the colder and wetter climate of the basin created a favourable niche for another type of forest, instead of savanna. The advance of dry vegetation was restricted to ecotonal conditions, preventing the formation of a continuous Pleistocene arc, predicted by Prado and Gibbs's hypothesis.     

Phylogeography of a widespread small carnivore,the western spotted skunk (Spilogale gracilis) reveals temporally variable signatures of isolation across western North America

We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre‐Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot. Putative climatic refugia resulting from Quaternary climate change were identified using paleoecological niche modeling and divergence dates compared to major vicariant events associated with Pre‐Pleistocene conditions. We recovered three major mitochondrial clades corresponding to western North America (California, Baja, and across the Great Basin), east‐central North America (Texas, central Mexico, New Mexico), and southwestern Arizona/northwestern Mexico. Time to most recent common ancestor for S. gracilis occurred ~1.36 Ma. Divergence times for each major clade occurred between 0.25 and 0.12 Ma, with signature of population expansion occurring 0.15 and 0.10 Ma. Ecological niche models identified three potential climatic refugia during the Last Interglacial, (1) west coast of California and Oregon, (2) northwestern Mexico, and (3) southern Texas/northeastern Mexico as well as two refugia during the Last Glacial Maximum, (1) western USA and (2) southern Texas/northeastern Mexico. This study supports PPD in shaping species‐level diversity compared to QCC‐driven changes at the intraspecific level for Spilogale, similar to the patterns reported for other small mammals (e.g., rodents and bats). Phylogeographic patterns also appear to have been shaped by both habitat and river vicariance, especially across the desert southwest. Further, continuing climate change during the Holocene coupled with anthropogenic modifications during the Anthropocene appears to be removing both of these barriers to current dispersal of western spotted skunks.     

Influences on koala habitat selection across four local government areas on the far north coast of NSW

Conserving habitats crucial for threatened koala (Phascolarctos cinereus) populations requires rating habitat quality from a fine spatial scale to patches, landscapes and then regions. The koala has a specialized diet focused on the leaves of a suite of Eucalyptus species. We asked: what are the key regional influences on habitat selection by koalas in the far north coast of New South Wales? We addressed this question by investigating the multi-scale factors, and within-scale and cross-scale interactions, that influence koala habitat selection and distribution across four local government areas on the far north coast of New South Wales. We assembled and analysed a large data set of tree selection, identified by the presence of scats, in a wide range of randomly selected 5 × 5 km grids across the region. This resulted in more than 9000 trees surveyed for evidence of koala use from 302 field sites, together with associated biophysical site features. The dominant factor influencing habitat use and koala occurrence was the distribution of five Eucalyptus species. Koalas were more likely to use medium-sized trees of these species where they occurred on soils with high levels of Colwell phosphorous. We also identified new interactions among the distribution of preferred tree species and soil phosphorous, and their distribution with the amount of suitable habitat in the surrounding landscape. Our study confirmed that non-preferred species of eucalypts and non-eucalypts are extensively used by koalas and form important components of koala habitat. This finding lends support to restoring a mosaic of koala-preferred tree species and other species recognized for their value as shelter. Our study has provided the ecological foundation for developing a novel regional-scale approach to the conservation of koalas, with adaptability to other wildlife species.     

Phylogeography,population genetics and distribution modelling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change

A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modelling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as a case study. We integrate phylogeographical and population genetic analyses and species distribution modelling to develop a broad view of its current condition and prognosis for conservation. We use genotyping‐by‐sequencing to characterize the genomes of 142 S. longii individuals from 20 populations distributed throughout its range (New Jersey to Nova Scotia). We measure the distribution of genetic diversity in the species and reconstruct its phylogeographical history using the snapp and rase models. Extant populations of S. longii originated from a single refugium south of the Laurentide ice sheet around 25 ka. The genetic diversity of S. longii is exceedingly low, populations exhibit little genetic structure and the species is slightly inbred. Projected climate scenarios indicate that nearly half of extant populations of S. longii will be exposed to unsuitable climate by 2070. Similar changes in suitable habitat will occur for many other northern ACPF species—centres of diversity will shift northward and Nova Scotia may become the last refuges for those species not extinguished.     

不同气候情景下四子柳的亚洲潜在地理分布格局变化预测

四子柳(Salix tetrasperma Roxb.)为杨柳科柳属为数不多的分布区扩展到热带的物种之一,广泛分布于华南和东南亚地区,但其生境破碎化较为严重。该物种具有较高的园林绿化价值和生态价值,预测不同气候情景下该物种的地理分布将为四子柳的资源开发和合理利用乃至柳属的起源和分化研究提供重要的科学依据。利用四子柳全面且精确的分布信息和高分辨率环境数据,基于Maxent模型和ArcGIS空间分析,构建其末次间冰期、末次盛冰期、当代以及未来(2050,2070)的潜在空间分布格局,评价环境因子对分布模型的重要性,定量确定未来受到威胁的适宜生境区域和面积。结果表明,四子柳目前的适宜生境面积为234.65×10~4 km~2,主要位于东亚、南亚和东南亚的热带地区,气温年较差和年均降水量是限制其分布的主要环境因子。总体而言,从冰期至未来,四子柳的分布中心有南北往返迁移的趋势。四子柳在末次盛冰期时向西北方向扩张并开始出现于热带地区,表明该物种开始适应热带气候,进入全新世中期以后种群收缩并退缩到云贵高原的河谷地区和印度尼西亚的平原区域。随着全球气候变暖,在不同二氧化碳浓度路径下2050年和2070年四子柳的潜在适生境有可能破碎化增加,建议对缅甸东部及中部成片减少的边缘群体进行实时监测。     

The crested newt Triturus cristatus recolonized temperate Eurasia from an extra‐Mediterranean glacial refugium

We assess the role of the Carpathians as an extra‐Mediterranean glacial refugium for the crested newt Triturus cristatus. We combine a multilocus phylogeography (one mitochondrial protein‐coding gene, three nuclear introns, and one major histocompatibility complex gene) with species distribution modelling (projected on current and Last Glacial Maximum climate layers). All genetic markers consistently show extensive genetic variation within and genetic depletion outside the Carpathians. The species distribution model suggests that most of the current range was unsuitable at the Last Glacial Maximum, but a small suitable area remained in the Carpathians. Triturus cristatus dramatically expanded its postglacial range, colonizing much of temperate Eurasia from a glacial refugium in the Carpathians. Within the Carpathians, T. cristatus persisted in multiple geographically discrete regions, providing further support for a Carpathian ‘refugia within refugia’ scenario. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 574–587.     

Inbreeding and disease avoidance in a free‐ranging koala population

Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex‐biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free‐ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free‐ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.     

Two Robin Populations

Capsule This study is the first ever documented evidence of an interglacial refugium during the Last Interglacial for birds in Anatolia and suggests the need of a re-examination of the effects of the Last Interglacial on the geographic distribution and genetic structure of species.

Aims We tested whether, in accordance with the ‘refugia within refugia’ model, multiple refugia existed for Kruper's Nuthatch Sitta krueperi during the Last Glacial Maximum or the species survived along the coastal belt of Anatolia through the Late Quaternary glacial–interglacial cycles.

Methods An ecological niche model was developed to predict the geographic distribution of Kruper's Nuthatch under reconstructed past (the Last Interglacial and the Last Glacial Maximum), present, and projected future bioclimatic conditions. Also, robust coalescent-based analyses were used to assess demographic events over the history of Kruper's Nuthatch.

Results Kruper's Nuthatch survived the Last Glacial Maximum almost along the coastal belt of Anatolia, but not in multiple refugia, and surprisingly, contrary to expectations, it survived the Last Interglacial in southern Anatolia, but not along the coastal belt of Anatolia.

Conclusion A kind of the ‘refugia within refugia’ model (i.e. the ‘refugium within refugium’ model) was supported because range shifts took place within Anatolia (itself also a refugium) for Kruper's Nuthatch.     

Ephemeral Pleistocene woodlands connect the dots for highland rattlesnakes of the Crotalus intermedius group

Aim To test how Pleistocene climatic changes affected diversification of the Crotalus intermedius species complex. Location Highlands of Mexico and the south‐western United States (Arizona). Methods We synthesize the matrilineal genealogy based on 2406 base pairs of mitochondrial DNA sequences, fossil‐calibrated molecular dating, reconstruction of ancestral geographic ranges, and climate‐based modelling of species distributions to evaluate the history of female dispersion. Results The presently fragmented distribution of the C. intermedius group is the result of both Neogene vicariance and Pleistocene pine–oak habitat fragmentation. Most lineages appear to have a Quaternary origin. The Sierra Madre del Sur and northern Sierra Madre Oriental are likely to have been colonized during this time. Species distribution models for the Last Glacial Maximum predict expansions of suitable habitat for taxa in the southern Sierra Madre Occidental and northern Sierra Madre Oriental. Main conclusions Lineage diversification in the C. intermedius group is a consequence of Pleistocene climate cycling. Distribution models for two sister taxa in the northern and southern Sierra Madre Occidental and northern Sierra Madre Oriental during the Last Glacial Maximum provide evidence for the expansion of pine–oak habitat across the Central Mexican Plateau. Downward displacement and subsequent expansions of highland vegetation across Mexico during cooler glacial cycles may have allowed dispersal between highlands, which resulted in contact between previously isolated taxa and the colonization of new habitats.     

Long‐term declines in multiple waterbird species in a tidal embayment,south‐east Australia

Worldwide, local extinctions and severe declines in waterbird densities are being reported from many important waterbird sites. Waterbird sites often exist as a network, collectively providing crucial habitat for different life history stages of different species. Therefore, population changes at one site may strongly influence others. In Australia, many waterbird species are highly mobile, and move rapidly over long distances in response to rainfall. Large tidal wetlands often serve as drought refugia or alternative breeding habitat for these species. These sites are also the migration terminus of many species of shorebirds that spend their non‐breeding season in Australia. One such site in south‐eastern Australia is Western Port, a Ramsar‐listed tidal embayment forming part of the East Asian–Australasian Shorebird Site Network. We measured waterbird population trends over nearly 40 years in Western Port to see whether changes showed consistent trends over time across multiple species. Thirty‐nine species were recorded often enough to allow an analysis of trends over time using dynamic linear models and, where appropriate, piecewise linear regression. Twenty‐two species had declined, including four species of duck, five species of fish‐eating bird (cormorants, terns and pelicans), one species each of grebe, gull and heron, and 10 species of shorebird. Only two species (Australian pied oystercatcher Haematopus longirostris and straw‐necked ibis Threskiornis spinicollis) increased significantly over the same time period. Patterns of decline in non‐migratory waterbirds may reflect diminishing wetland availability, local reductions in fish prey, increased predation pressure and changes in inland wetland resources. Declines in migratory shorebirds are most likely related to loss of habitat elsewhere in their trans‐equatorial migration routes. These trends in waterbirds that use Western Port reflect widespread impacts on populations elsewhere in Australia and overseas, necessitating more than simply local management of this tidal embayment.     

Genome-wide SNP loci reveal novel insights into koala (<Emphasis Type="Italic">Phascolarctos cinereus</Emphasis>) population variability across its range

The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (F_ST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average F_ST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.