Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

‘Key biodiversity areas'' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site''s share of a threatened species'' population; expand these to include the proportion of the species'' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species'' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.     

Rhytidium rugosum (Bryophyta) colonized Scandinavia from at least two glacial refugial source populations

The Scandinavian post‐glacial history of the moss Rhytidium rugosum is traced on the basis of information from the nuclear markers ITS and gpd for 229 Scandinavian and 81 other specimens. Some haplotypes, groups or lineages identified in a NeighborNet split network are predominantly northern Scandinavian, whereas others are southern. With the distributions of individual haplotypes and the timing of the deglaciation in different parts of Scandinavia, this implies colonization from the south and from the north or north‐east. High haplotype and nucleotide diversity and the occurrence of certain private haplotypes in the north suggest that the species may have survived the Last Glacial Maximum in local refugia. Slightly higher numbers of private haplotypes in Scandinavia than in central or north‐eastern Europe also favour an explanation with at least some local glacial survival. Low diversity in the southernmost contiguous region of the Scandinavian mountain range is probably a result of recent land uplift and late colonization. The Scandinavian lowland regional populations probably represent remains of an earlier widespread population that became increasingly restricted to small and isolated areas when the vegetation closed during the post‐glacial period. Some of the lowland populations require extensive management to survive. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 635–657.     

A review of the subspecies status of the Icelandic Purple Sandpiper Calidris maritima littoralis

The Icelandic Purple Sandpiper Calidris maritima littoralis (C.L. Brehm, 1831) represents one member of a poorly understood subspecies complex. Currently, differences in size define two other subspecies: Calidris maritima belcheri Engelmoer & Roselaar, 1998, which breeds in north‐eastern Canada along the Hudson Bay and James Bay, and Calidris maritima maritima (Brunnich, 1764), which breeds along the Arctic coasts elsewhere in northern Canada, Greenland, Svalbard, Scotland, and Fennoscandia, to northern central Siberia. There are large size differences amongst populations of C. m. maritima, however. As an Arctic/Alpine breeding bird, C. m. littoralis could provide an interesting perspective on the evolutionary changes following a northwards expansion of a species after glacial retreat. Considering the extent of the ice sheet in the northern hemisphere during the last glaciation, and the short period of time since it ended, the correct attribution of subspecies status for C. m. maritima may reflect either rapid diversification from a single population or ancestral splits of distinct evolutionary lineages that survived in isolation at southern latitudes. We applied morphometric subspecies criteria, diagnosability by Amadon's rule, and genetic analysis of five nuclear introns, and the mitochondrial DNA markers cytochrome oxidase c subunit I (COI) and NADH dehydrogenase subunit 2 (ND2), to geographically separate breeding populations in order to examine the subspecies status of the Icelandic population. The results do not provide support for the subspecies status of the Icelandic population because the nominate and Icelandic subspecies fail to uphold Amadon's rule, and genetic analyses indicate that the study populations derive from a single shared refugium. © 2015 The Linnean Society of London     

Reef‐coral refugia in a rapidly changing ocean

This study sought to identify climate‐change thermal‐stress refugia for reef corals in the Indian and Pacific Oceans. A species distribution modeling approach was used to identify refugia for 12 coral species that differed considerably in their local response to thermal stress. We hypothesized that the local response of coral species to thermal stress might be similarly reflected as a regional response to climate change. We assessed the contemporary geographic range of each species and determined their temperature and irradiance preferences using a k‐fold algorithm to randomly select training and evaluation sites. That information was applied to downscaled outputs of global climate models to predict where each species is likely to exist by the year 2100. Our model was run with and without a 1 °C capacity to adapt to the rising ocean temperature. The results show a positive exponential relationship between the current area of habitat that coral species occupy and the predicted area of habitat that they will occupy by 2100. There was considerable decoupling between scales of response, however, and with further ocean warming some ‘winners’ at local scales will likely become ‘losers’ at regional scales. We predicted that nine of the 12 species examined will lose 24–50% of their current habitat. Most reductions are predicted to occur between the latitudes 5–15°, in both hemispheres. Yet when we modeled a 1 °C capacity to adapt, two ubiquitous species, Acropora hyacinthus and Acropora digitifera, were predicted to retain much of their current habitat. By contrast, the thermally tolerant Porites lobata is expected to increase its current distribution by 14%, particularly southward along the east and west coasts of Australia. Five areas were identified as Indian Ocean refugia, and seven areas were identified as Pacific Ocean refugia for reef corals under climate change. All 12 of these reef‐coral refugia deserve high‐conservation status.     

The cold‐water climate shield: delineating refugia for preserving salmonid fishes through the 21st century

The distribution and future fate of ectothermic organisms in a warming world will be dictated by thermalscapes across landscapes. That is particularly true for stream fishes and cold‐water species like trout, salmon, and char that are already constrained to high elevations and latitudes. The extreme climates in those environments also preclude invasions by most non‐native species, so identifying especially cold habitats capable of absorbing future climate change while still supporting native populations would highlight important refugia. By coupling crowd‐sourced biological datasets with high‐resolution stream temperature scenarios, we delineate network refugia across >250 000 stream km in the Northern Rocky Mountains for two native salmonids—bull trout (BT) and cutthroat trout (CT). Under both moderate and extreme climate change scenarios, refugia with high probabilities of trout population occupancy (>0.9) were predicted to exist (33–68 BT refugia; 917–1425 CT refugia). Most refugia are on public lands (>90%) where few currently have protected status in National Parks or Wilderness Areas (<15%). Forecasts of refuge locations could enable protection of key watersheds and provide a foundation for climate smart planning of conservation networks. Using cold water as a ‘climate shield’ is generalizable to other species and geographic areas because it has a strong physiological basis, relies on nationally available geospatial data, and mines existing biological datasets. Importantly, the approach creates a framework to integrate data contributed by many individuals and resource agencies, and a process that strengthens the collaborative and social networks needed to preserve many cold‐water fish populations through the 21st century.     

Phylogeography and genetic structure of the red-legged partridge (Alectoris rufa): more evidence for refugia within the Iberian glacial refugium

The Pleistocene climatic oscillations promoted the diversification in avian species during the last glacial period. The red‐legged partridge (Alectoris rufa, Family Phasianidae) has a large natural distribution extending from the Mediterranean to humid temperate zones. However, the genetic structure for this species is unknown. The present study investigates the phylogeography, genetic structure and demographic history of A. rufa across its distribution, employing both mitochondrial DNA control region sequences and nuclear microsatellite loci. Our results propose that this species was greatly affected by Pleistocene glaciations. The mismatch analyses suggest that the current populations resulted from post‐glacial expansion and subsequent differentiation resulting in five diagnosable genetic clusters: Southwestern, Central‐eastern, Northwestern, Balearic and French and Italian. Further, we found evidence of three glacial refugia within the currently recognized Iberian glacial refugium. The intraspecific structure revealed by both maternal and biparental phylogeographic analyses was not resolved in the phylogenetic analyses. Based on all considerations, we recommended that five management units be recognized.     

Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis

Phylogeographic studies provide critical insight into the evolutionary histories of model organisms; yet, to date, range-wide data are lacking for the rough periwinkle Littorina saxatilis, a classic example of marine sympatric speciation. Here, we use mitochondrial DNA (mtDNA) sequence data to demonstrate that L. saxatilis is not monophyletic for this marker, but is composed of two distinct mtDNA lineages (I and II) that are shared with sister species Littorina arcana and Littorina compressa. Bayesian coalescent dating and phylogeographic patterns indicate that both L. saxatilis lineages originated in the eastern North Atlantic, around the British Isles, at approximately 0.64 Ma. Both lineages are now distributed broadly across the eastern, central and western North Atlantic, and show strong phylogeographic structure among regions. The Iberian Peninsula is genetically distinct, suggesting prolonged isolation from northeastern North Atlantic populations. Western North Atlantic populations of L. saxatilis lineages I and II predate the last glacial maximum and have been isolated from eastern North Atlantic populations since that time. This identification of two distinct, broadly distributed mtDNA lineages further complicates observed patterns of repeated incipient ecological speciation in L. saxatilis, because the sympatric origins of distinct ecotype pairs on eastern North Atlantic shores may be confounded by admixture of divergent lineages.     

A climatic basis for microrefugia: the influence of terrain on climate

There is compelling evidence from glacial and interglacial periods of the Quaternary of the utilization of microrefugia. Microrefugia are sites that support locally favorable climates amidst unfavorable regional climates, which allow populations of species to persist outside of their main distributions. Knowledge of the location of microrefugia has important implications for climate change research as it will influence our understanding of the spatial distribution of species through time, their patterns of genetic diversity, and potential dispersal rates in response to climate shifts. Indeed, the implications of microrefugia are profound and yet we know surprisingly little about their climatic basis; what climatic processes can support their subsistence, where they may occur, their climatic traits, and the relevance of these locations for climate change research. Here I examine the climatic basis for microrefugia and assert that the interaction between regional advective influences and local terrain influences will define the distribution and nature of microrefugia. I review the climatic processes that can support their subsistence and from this climatic basis: (1) infer traits of the spatial distribution of microrefugia and how this may change through time; (2) review assertions about their landscape position and what it can tell us about regional climates; and (3) demonstrate an approach to forecasting where microrefugia may occur in the future. This synthesis highlights the importance of landscape physiography in shaping the adaptive response of biota to climate change.     

Environmental dependence of population dynamics and height growth of a subalpine conifer across its vertical distribution: an approach using high‐resolution aerial photographs

Many studies have reported shifts in the altitudinal ranges of plant species in response to recent global warming. However, most studies of tree species have been conducted on a small scale and have focused on tree line ecotones by examining tree rings and age structure on account of the long life spans of the trees. To examine the impact of climate change on forest dynamics at a regional scale, we investigated differences in the population density and canopy height of a Japanese subalpine coniferous species, Abies mariesii, between 1967 and 2003 by analysis of high‐resolution aerial photographs of the Hakkoda Mountains, Honshu, Japan. In 712 plots within the photographs we analyzed which environmental variables (including elevation, aspect, wetness, and distance from moorlands) account for these changes. The population density of A. mariesii decreased below 1000 m a.s.l. and increased above 1300 m a.s.l. It also increased around moorlands, which may provide refugia at low elevations. The rate of increase in canopy height was lowest on the southeastern slopes and on the periphery of the moorlands. The distinct changes in the population density of A. mariesii at its distribution limits probably reflect the responses of the population to climatic changes during three decades. Areas surrounding the moorlands may offer refugia in spite of the poor growing conditions there.     

Flow- and substratum-mediated movement by a stream insect

1. In streams subject to frequent hydrologic disturbance, the ability of benthic invertebrates to disperse within the channel is key to understanding the mechanisms of flow refugium use and population persistence. This study focuses on crawling invertebrates, the effects on movement of abiotic factors (specifically, flow near the stream bed and bed micro‐topography) and the consequences for dispersal. 2. In a large flume, we observed individual cased caddisflies, Potamophylax latipennis, moving in fully turbulent flows over a precise replica of a water‐worked surface. From maps of movement paths, we quantified crawling behaviour and entrainment, and the influence of bed micro‐topography. We manipulated discharge and tested its effect on movement, linear displacement and areal dispersal. The highest discharge treatment was a disturbance to the caddis; the lowest discharge was not. Crawling behaviours were used to parameterise random walk models and estimate population dispersal, and to test the effects of abiotic factors on movement. 3. Bed micro‐topography influenced crawling in several ways. Caddis spent most of their time at the junctions between proud particles and the adjacent plane bed. The frequency distribution of turn angles was bimodal, with modal values approximating the angle required to travel around median‐sized particles. Larvae generally crawled downstream, but crawling direction relative to the flow was skewed by bed micro‐topography and was not directly downstream, unlike drift. 4. Caddis crawled for most of the time and discharge affected almost every aspect of their movement. As discharge increased, caddis crawled less often, more slowly and over shorter distances; they also became entrained more frequently and over greater distances. With increased discharge, caddis spent proportionately less time at the junctions between proud particles and the adjacent plane bed, and more time on the tops and sides of proud clasts. This is curious as most entrainment occurred from the tops and sides of clasts and entrainment is generally considered to be disadvantageous during disturbances. 5. Linear displacement (drift and entrainment combined) was downstream, but the relation between total displacement and discharge was complex. Total displacement decreased at intermediate discharge as crawling decreased, but increased at high discharge as entrainment and drift played a greater role in movement. 6. Within‐stream dispersal via crawling contained elements of both a correlated random walk (we observed directional persistence in turn angles) and a biased random walk (we observed downstream bias in move direction angles) and was best described as a biased correlated random walk. Dispersal was inversely related to discharge, suggesting that the ability of P. latipennis to crawl into flow refugia on the streambed is reduced at high flow.