High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonisation in bar-tailed godwits.

In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non-stop flights of any landbird. Using nextRAD sequencing of 14,318 single-nucleotide polymorphisms and scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in two main lineages at the last glacial maximum, when much of their present-day breeding range persisted in a vast, unglaciated Siberian-Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine-scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non-breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations.

Genetic Diversity and Phylogeography of the Relict Tree Fern Culcita macrocarpa: Influence of Clonality and Breeding System on Genetic Variation.

The tree fern Culcita macrocarpa, a threatened Iberian-Macaronesian endemism, represents the sole European species of the order Cyatheales. Considered a Tertiary relict of European Palaeotropical flora, its evolutionary history and genetic diversity, potentially influenced by presumed high clonal propagation, remain largely unknown. This study elucidates the phylogeographic history of C. macrocarpa, assessing the impact of vegetative reproduction on population dynamics and genetic variability. We provide genetic data from eight newly identified nuclear microsatellite loci and one plastid DNA region for 17 populations spanning the species' range, together with species distribution modeling data. Microsatellites reveal pervasive clonality in C. macrocarpa, which has varied among populations. We assess the impact of clonality on genetic diversity and evaluate how estimates of intra-population genetic diversity indices and genetic structuring are affected by the chosen definition of "individual" (focusing exclusively on genetically distinct individuals, genets, as opposed to considering all independent clonal replicates, ramets). We identify two main population groups, one in the northern Iberian Peninsula and the other in the Macaronesian archipelagos and southern Iberian Peninsula. Within each group, we found relict populations (in the Azores and the Cantabrian Cornice) as well as recent originated populations. This population structure suggests colonization dynamics in which recent populations originated from one or a few genets of relict populations and became established through intra-gametophytic self-fertilization and vegetative expansion. DAPC analysis facilitated the identification of alleles that most significantly contributed to the observed population structure. The current Andalusian populations appear to have originated from colonization events from the Azores and the Cantabrian Cornice. Our findings suggest that C. macrocarpa persisted through the Last Glacial Maximum in two refugia: the Azores and the Cantabrian Cornice. Colonization into new areas occurred presumably from these refuges, generating two large population groups with structured genetic diversity. This study underscores the significance of clonality in establishing new populations and shaping genetic structure.

Central China as LGM plant refugia: Insights from biome reconstruction for palaeoclimate information.

The demonstration of survival of forest stands in relatively stable refugia during cold glacial stages has offered an increased understanding of the response of vegetation to climate change, but also provides insight into considerations for the conversation of biodiversity hotspots. However, refugia studies in China remain in question due to the lack of plant macrofossils, especially those of endemic and relict species. Palynology, while more broad brush, provides a method for exploring whether refugia occur, and can provide some details of palaeovegetation composition and temporal dynamics. Here, three pollen records derived from subalpine wetlands in central China, spanning the Last Glacial Maximum (LGM), have been coupled with biome and mean annual precipitation (MAP) reconstructions to identify the presence of trees that endured cold climate. The results indicated that some forest, including temperate deciduous broadleaf forest and cool mixed forest, survived the LGM at the three locations, and was thus at odds with the hypothesis that forests were replaced by herbs and grasses in central China at that time. Refugia favored by protection from cold air drainage and the availability of adequate water can explain the survival of the trees during otherwise harsh episodes. Our findings are consistent with other records from central China that argue for tree dominated refugia during the LGM.

Decametric-scale buffering of climate extremes in forest understory within a riparian microrefugia: the key role of microtopography.

Riparian corridors often act as low-land climate refugia for temperate tree species in their southern distribution range. A plausible mechanism is the buffering of regional climate extremes by local physiographic and biotic factors. We tested this idea using a 3-year-long microclimate dataset collected along the Ciron river, a refugia for European beech (Fagus sylvatica) in southwestern France. Across the whole network, canopy gap fraction was the main predictor for spatial microclimatic variations, together with two other landscape features (elevation above the river and woodland fraction within a 300m radius). However, within the riparian forest only (canopy gap fraction < 25%, distance to the river < 150m), variations of up to -4°C and + 15% in summertime daily maximum air temperature and minimum relative humidity, respectively, were still found from the plateau to the cooler, moister river banks, only ~ 5-10m below. Elevation above the river was then identified as the main predictor, and explained the marked variations from the plateau to the banks much better than canopy gap fraction. The microclimate measured near the river is as cool but moister than the macroclimate encountered at 700-1000m asl further east in F. sylvatica's main distribution range. Indeed, at all locations, we found that air relative humidity was higher than expected from a temperature-only effect, suggesting that extra moisture is brought by the river. Our results explain well why beech trees in this climate refugium are restricted to the river gorges where microtopographic variations are the strongest and canopy gaps are rare.

Topography-driven microclimate gradients shape forest structure, diversity, and composition in a temperate refugial forest.

Macroclimate drives vegetation distributions, but fine-scale topographic variation can generate microclimate refugia for plant persistence in unsuitable areas. However, we lack quantitative descriptions of topography-driven microclimatic variation and how it shapes forest structure, diversity, and composition. We hypothesized that topographic variation and the presence of the forest overstory cause spatiotemporal microclimate variation affecting tree performance, causing forest structure, diversity, and composition to vary with topography and microclimate, and topography and the overstory to buffer microclimate. In a 20.2-ha inventory plot in the North American Great Plains, we censused woody stems ≥1 cm in diameter and collected detailed topographic and microclimatic data. Across 59-m of elevation, microclimate covaried with topography to create a sharp desiccation gradient, and topography and the overstory buffered understory microclimate. The magnitude of microclimatic variation mirrored that of regional-scale variation: with increasing elevation, there was a decrease in soil moisture corresponding to the difference across ~2.1° of longitude along the east-to-west aridity gradient and an increase in air temperature corresponding to the difference across ~2.7° of latitude along the north-to-south gradient. More complex forest structure and higher diversity occurred in moister, less-exposed habitats, and species occupied distinct topographic niches. Our study demonstrates how topographic and microclimatic gradients structure forests in putative climate-change refugia, by revealing ecological processes enabling populations to be maintained during periods of unfavorable macroclimate.

Predictable patterns within the kelp forest can indirectly create temporary refugia from ocean acidification.

Kelps are recognized for providing many ecosystem services in coastal areas and considered in ocean acidification (OA) mitigation. However, assessing OA modification requires an understanding of the multiple parameters involved in carbonate chemistry, especially in highly dynamic systems. We studied the effects of sugar kelp (Saccharina latissima) on an experimental farm at the north end of Hood Canal, Washington-a low retentive coastal system. In this field mesocosm study, two oyster species (Magallana gigas, Ostrea lurida) were exposed at locations in the mid, edge, and outside the kelp array. The Hood Head Sugar Kelp Farm Model outputs were used to identify dominating factors in spatial and temporal kelp dynamics, while wavelet spectrum analyses helped in understanding predictability patterns. This was linked to the measured biological responses (dissolution, growth, isotopes) of the exposed organisms. Positioned in an area of high (sub)-diel tidal fluxes with low retention potential, there were no measurable alterations of the seawater pH at the study site, demonstrating that the kelp array could not induce a direct mitigating effect against OA. However, beneficial responses in calcifiers were still observed, which are linked to two causes: increased pH predictability and improved provisioning through kelp-derived particulate organic resource utilization and as such, kelp improved habitat suitability and indirectly created refugia against OA. This study can serve as an analogue for many coastal bay habitats where prevailing physical forcing drives chemical changes. Future macrophyte studies that investigate OA mitigating effects should focus also on the importance of predictability patterns, which can additionally improve the conditions for marine calcifiers and ecosystem services vulnerable to or compromised by OA, including aquaculture sustainability.

Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens).

BACKGROUND: There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity. RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks. CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.

Cushions serve as conservation refuges for the Himalayan alpine plant diversity: Implications for nature-based environmental management.

Globally, rapid climate and land-use changes in alpine environments are posing severe risks to their bountiful biodiversity and ecosystem services. Currently, nature-based solutions are fast-emerging as the preferred approach to address the challenges of environmental sustainability. In alpine environments, cushion plants owing to their unique architecture and adaptability offer a potential nature-based system to plan biodiversity conservation and habitat restoration strategies. Here, we employed an analytical framework to test whether and how the cushion plants facilitate the sustenance of alpine plant diversity in Kashmir Himalaya. We specifically aimed to answer: what are the effects of the cushion plants on the patterns of alpine species richness and phylogenetic diversity, and whether these effects vary across spatial scales (local versus landscape), cushion types, and changing elevation. We randomly selected pairs of cushion and neighbouring non-cushion plots (size 100 m2) across 34 different alpine sites in the study region. Within each plot, we randomly laid three 5 m2 quadrats for vegetation sampling, and sampled a total of 204 quadrats in 68 plots with seven cushion types along elevation ranging from 3100 to 3850 m. Our results revealed positive effects of the cushions by supporting a higher community species richness (SR) and phylogenetic diversity (PD). The effects were consistent both at the local (i.e., quadrat) and landscape (i.e., plot) scales, but varied significantly with the cushion type. Interestingly, SR and PD showed an increasing trend with increase in elevation in cushion communities, thereby supporting stress gradient hypothesis. Along the elevational gradient, the cushion communities showed phylogenetic overdispersion, but clustering by non-cushions. Overall, our study provides empirical evidence to reinforce the role of the cushions as conservation refugia for an imperilled alpine plant diversity in the Himalaya. Looking ahead, we highlight the far-reaching implications of our findings in guiding the nature-based environmental management of alpine ecosystems worldwide.

How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders.

Large-scale barcoding projects help to aggregate information on genetic variability of multiple species throughout their ranges. Comparing DNA sequences of both non-conspecific and conspecific individuals from distant parts of their ranges helps to compare level of genetic isolation-by-distance patterns in different species and adaptive types. We compared mitochondrial CO1 gene sequences of 223 spiders from Georgia (Caucasus), representing 124 species and eight families, with 3097 homological sequences from spiders mostly from Europe, but also from other parts of the World. In most families, a significant isolation-by distance pattern was observed on family level. On species level, a significant isolation-by-distance was observed in 40 species, although this low proportion is most likely related to a lack of data. Simultaneously, remarkable differences in spatial structure were shown for different species. Although the majority of the studied species have a broad western Palearctic range, web-building spiders from families Araneidae, Theridiidae, and Linyphiidae are less isolated spatially than flower spiders (Thomisidae), jumping spiders (Salticidae), wolf spiders (Lycosidae), sac spiders (Clubionidae), and ground spiders (Gnaphosidae). This pattern is related with more common ballooning in web building than in actively hunting spiders, which commonly remain isolated since preglacial time. Ground spiders build the most isolated populations in the Caucasus.

The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China.

Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.

The phylogenetic relationship and demographic history of rhesus macaques (Macaca mulatta) in subtropical and temperate regions, China.

Pleistocene climatic oscillations exerted significant influences on the genetic structure and demography of rhesus macaque (Macaca mulatta) in eastern China. However, the evolutionary history of rhesus macaques in subtropical and temperate China remained unclear and/or controversial. Herein, we analyzed the autosomes, mitochondrial genomes, and Y-chromosomes from 84 individuals of Chinese rhesus macaque. The results revealed that (1) all individuals were clustered into pan-west and pan-east genetic groups, which exhibited Shaanxi Province as the northernmost region of western dispersal route of rhesus macaques in China; (2) in subtropical and temperate China, rhesus macaques were divided into four lineages (TH, DB, HS, and QL), and their divergence times corresponded to the Penultimate Glaciation (300-130 kya) and Last Glaciation (70-10 kya), respectively; (3) the individuals from Mt. Taihangshan (TH) are closely related to individuals from Mt. Dabashan (DB) in the autosomal tree, rather than individuals from Mt. Huangshan (HS) as indicated by the mitogenome tree, which supports the hypothesis that the ancestral rhesus macaques radiated into Mt. Taihangshan from Mt. Huangshan via Mt. Dabashan; and (4) the demographic scenario of the four lineages showed the ancestral rhesus macaques bottleneck and expansion corresponding to the suitable habitat reduction and expansion, which confirmed they had experienced northward recolonization and southward retreat events from Mt. Huangshan area via Northern China Plain to Northernmost China along with Pleistocene glacial cycles. This study provides a new insight into understanding how Pleistocene glaciation has influenced faunal diversity in subtropical and temperate China, especially for those exhibiting differential patterns of sex dispersal.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

PREMISE: Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. METHODS: We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. RESULTS: We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. CONCLUSIONS: Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

Assessing phenotypic variation and plasticity of endemic gastropods from thermal water refugia using complex morphometric techniques: A case study of Lake Pețea melanopsids.

Understanding the underlying reasons for phenotypic plasticity and resulting morphological disparity is one of the key topics of evolutionary research. The phenotypic plasticity of extant and fossil melanopsids has been widely documented. Yet millennial-resolution, well-dated records from small aquatic habitats harboring endemics are scarce. The thermal spring-fed Lake Pețea is an ice age refugia harboring a unique endemic warm-water fauna. Subfossil melanopsids display incredible morphological variability from smooth to keeled, elongated to ribbed, shouldered forms. Numerous morphotypes have been considered as individual taxa with a fluent succession from the smooth elongated to the ribbed, shouldered types. This study presents an extensive morphometric analysis of subfossil melanopsids (ca. 3500 specimens) derived from stratified samples with an independent chronology. The aim was to separate morphotypes for investigations of temporal morphological disparity. Our results challenge the widely accepted hypothesis that proposes the evolution of shouldered, compressed, ribbed shells through a two-step process from smooth elongated spindle-shaped shells. Instead, it suggests that the subfossil shells belong to two distinct taxa present throughout the available stratigraphic data. The main components of shape variation, shape globularity, and shell coiling seem allometry-related. Ribs, striation, and keels appear randomly. High-spired spindle-shaped forms were considered to represent specimens of Microcolpia daudebartii hazayi. Bulkier low-spired and shouldered specimens represent phenotypes of Mi. parreyssii parreyssii. The collective and random distribution of morphotypes from the early stages of the lake's history also refutes the idea of a continuous transformation of the elongated forms into compressed, shouldered ones. Rather points to multiple events and environmental stimuli triggering development. Melanopsids appear in Late Glacial horizons, with Theodoxus prevostianus preferring temperatures above 23°C which may indicate the subordinate presence of hot water microhabitats in cooler waters.

The Silk roads: phylogeography of Central Asian dice snakes (Serpentes: Natricidae) shaped by rivers in deserts and mountain valleys.

Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.

Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa.

Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.

Latitude or altitude as the future refugium? A case for the future of forests in Asia Minor and its surroundings.

At the current juncture with climate change, centennial projections of species distributions in biodiversity hotspots, using dynamic vegetation models may provide vital insight into conservation efforts. This study aims to answer: (1) if climate change progresses under a business-as-usual scenario of anthropogenic emissions for this century, how may the forest ranges be affected? (2) will there be potential regional extinctions of the taxa simulated? (3) may any site emerge as a potential refugium? STUDY AREA: Anatolian Peninsula and its surroundings, longitudes 24-50° E, latitudes 33-46° N. Time Period: 1961-2100. Major Taxa Studied: 25 woody species and a C3 grass-type. METHOD: Keeping a spatial window large enough to track potential changes in the vegetation range and composition especially in the mountain ranges within the study area, we parameterized a process-based regional-to-global dynamic vegetation model (LPJ-GUESS v 4.1), forced it with ERA5-Land reanalysis for the historical period, and five different bias-corrected centennial global circulation model (GCM) datasets under SSP5-8.5, and simulated the dynamic responses of key forest species. Bivariate spatio-temporal maps from the simulation results were constructed for final analysis. RESULTS: A significant increase in woody taxa biomass for the majority of our study area, towards the end of the century was simulated, where temperate taxa with high tolerance for drought and a wider range of temperatures took dominance. The mountain ranges in our study area stood out as critical potential refugia for cold favoring species. There were no regional extinctions of taxa, however, important changes in areal dominance and potential future forest composition were simulated. MAIN CONCLUSIONS: Our simulation results suggest a high potential for future forest cover in our study region by the end of the century under a high emissions scenario, sans human presence, with important changes in vegetation composition, including encroachment of grasslands ecosystems by woody taxa.

Where east meets west: Phylogeography of the high Arctic North American brant goose.

Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.

Legacies of millennial-scale climate oscillations in contemporary biodiversity in eastern North America.

The Atlantic meridional overturning circulation (AMOC) has caused significant climate changes over the past 90 000 years. Prior work has hypothesized that these millennial-scale climate variations effected past and contemporary biodiversity, but the effects are understudied. Moreover, few biogeographic models have accounted for uncertainties in palaeoclimatic simulations of millennial-scale variability. We examine whether refuges from millennial-scale climate oscillations have left detectable legacies in the patterns of contemporary species richness in eastern North America. We analyse 13 palaeoclimate estimates from climate simulations and proxy-based reconstructions as predictors for the contemporary richness of amphibians, passerine birds, mammals, reptiles and trees. Results suggest that past climate changes owing to AMOC variations have left weak but detectable imprints on the contemporary richness of mammals and trees. High temperature stability, precipitation increase, and an apparent climate fulcrum in the southeastern United States across millennial-scale climate oscillations aligns with high biodiversity in the region. These findings support the hypothesis that the southeastern United States may have acted as a biodiversity refuge. However, for some taxa, the strength and direction of palaeoclimate-richness relationships varies among different palaeoclimate estimates, pointing to the importance of palaeoclimatic ensembles and the need for caution when basing biogeographic interpretations on individual palaeoclimate simulations. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Climate change impacts on mesophotic regions of the Great Barrier Reef.

Climate change projections for coral reefs are founded exclusively on sea surface temperatures (SST). While SST projections are relevant for the shallowest reefs, neglecting ocean stratification overlooks the striking differences in temperature experienced by deeper reefs for all or part of the year. Density stratification creates a buoyancy barrier partitioning the upper and lower parts of the water column. Here, we mechanistically downscale climate models and quantify patterns of thermal stratification above mesophotic corals (depth 30 to 50 m) of the Great Barrier Reef (GBR). Stratification insulates many offshore regions of the GBR from heatwaves at the surface. However, this protection is lost once global average temperatures exceed ~3 °C above preindustrial, after which mesophotic temperatures surpass a recognized threshold of 30 °C for coral mortality. Bottom temperatures on the GBR (30 to 50 m) from 2050 to 2060 are estimated to increase by ~0.5 to 1 °C under lower climate emissions (SSP1-1.9) and ~1.2 to 1.7 °C under higher climate emissions (SSP5-8.5). In short, mesophotic coral reefs are also threatened by climate change and research might prioritize the sensitivity of such corals to stress.

Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus).

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.