A western representative of an eastern clade: phylogeographic history of the gypsophilous plant Nepeta hispanica

The preference of certain plant species for gypsum soils leads to disjunct population structures that are thought to generate island-like dynamics potentially influencing biogeographic patterns at multiple evolutionary scales. Here, we study the evolutionary and biogeographic history of Nepeta hispanica, a western Mediterranean plant associated with gypsum soils and displaying a patchy distribution with populations very distant from each other. Three approaches were used: (a) interspecific phylogenetic analyses based on nuclear DNA sequences of the ITS region to unveil the relationships and times of divergence between N. hispanica and its closest relatives; (b) phylogeographic analyses using plastid DNA regions trnS-trnG and psbJ-petA to evaluate the degree of genetic isolation between populations of N. hispanica, their relationships and their genetic diversity; and (c) ecological niche modelling to evaluate historical distributional changes. Results reveal that N. hispanica belongs to an eastern Mediterranean and Asian clade diversified in arid environments since the Miocene-Pliocene. This species represents the only extant lineage of this clade that colonized the western Mediterranean, probably through the northern Mediterranean coast (southern Europe). Present Iberian populations display a high plastid genetic diversity and, even if geographically distant from each other, they are highly connected according to the distribution of plastid haplotypes and lineages. This can be explained by a scenario involving a complex history of back-and-forth colonisation events, facilitated by a relative stability of suitable conditions for the species across the Iberian Peninsula throughout the Quaternary.

Demographic history and range modelling of the East Mediterranean Abies cilicica

The Mediterranean Basin is one of the 36 global hotspots of biodiversity and it is rich in endemic tree species. The complex geological history of the region throughout the Neogene and Quaternary periods that were marked with several palaeoclimatic transformations was a major factor triggering the genetic divergence of lineages in tree species in the region. The ongoing global climate change is the main factor threatening Mediterranean biodiversity. The risk of population decline related to aridization is the highest in the case of endemics, especially for cold-adapted conifers, such as Abies cilicica. The Cilician fir grows in the East Mediterranean mountains that constitute a local centre of endemism within the region. The species range is fragmented and small-size populations prevail. Previous studies have suggested that the last glacial cycle led to a significant reduction in the species range and might have initiated genetic divergence. As a result, two lineages are currently recognized at the subspecies level, A. cilicica subsp. isaurica (Turkey) and A. cilicica subsp. cilicica (Turkey, Syria, and Lebanon). The predictions about the impact of future climate changes in the East Mediterranean suggest a profound reduction of precipitation and overall warming that may put the remnant populations of A. cilicica at a risk of decline. Here, we used the Bayesian approach to investigate the demographic history of endemic A. cilicica. Specifically, we estimated the probable time of the intraspecies divergence to verify previous assumptions about the species’ evolutionary history. Additionally, niche modelling was used to outline the potential range of changes in the past and to indicate glacial refugia in where the species persisted climate crisis. This approach was also used to explore the possible influence of the future climate changes on the distribution of A. cilicica in the region. Our results demonstrate that the divergence between the Lebanese and the Turkish populations that occurred ~220 ka years BP coincided with the Riss glaciation. According to palaeoecological data, in the East Mediterranean, that glacial period caused a severe reduction in the populations of woody species due to the aridity of the climate. At that time, the Lebanese-Syrian part of the range was likely disconnected from the main range. The second split was induced by the last glacial cycle ~60 ka years BP and led to the separation of the Central Taurus and East Taurus population and, consequently, to the formation of the two subspecies. Niche modelling for the last glacial maximum has allowed us to locate the probable refugia for A. cilicica in the western Anatolia and Syria-Lebanon area. A projection of the future possible distribution of the species indicates a serious reduction of the range during this century.

An Overview of Historical Distribution Patterns of Chalcides ocellatus (Forsskål, 1775) Using Ecological Niche Modelling: the Taurus Mountains as a Refugium

The Taurus Mountains that have a very rich biodiversity are one of the most important mountain chains in Anatolia. In this study, we examined distribution patterns of Chalcides ocellatus that has a restricted dispersal between the Taurus Mountains from the past to current using ecological niche modeling. The Taurus Mountains have played the role as a refugium area in which C. ocellatus could survive through a period of unfavorable conditions. Especially in the glaciation period, Amanos Mountains in the Middle Taurus as an isolating barrier appeared unsuitable habitats for the lineages of C. ocellatus. This indicated that the lineages of C. ocellatus were formed as a result of habitat fragmentation during the last glacial maximum and last interglacial, and were consequently adapted to different climatic conditions.

Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that since SARS-CoV-2 emergence several closely-related viruses have been discovered and sarbecovirus-host interactions have gained attention. We assess sampling biases and model bats' current distributions based on climate and landscape relationships and project future scenarios. The most important predictors of species distribution were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in >2 °C hotter locations in a fossil-fueled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.

Species monitoring through space and time — combining microfluidic SNP genotyping and environmental niche modelling on herbarium specimens of the rare Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae)

Aim: We have studied population genetic change through time in the Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae); a plant species that has experienced a drastic population decline and habitat loss in Europe. We aimed at adding a historic level to the monitoring of dragonhead by testing a microfluidic SNP array approach on herbarium specimens up to 200 years old and comparing the genomic results with that of modern populations in Norway. We also aimed to gain a more holistic species knowledge to guide monitoring efforts by combining herbarium genomics with ecological niche modelling (ENM). Location: Europe (mainly Norway) Methods: We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008. Obtained genotype data were compared with SNP data from modern samples using various population genetic analyses. We used sample metadata and observational records to model the species’ environmental niche. Results: The SNP array successfully genotyped all included herbarium specimens but was less capable of capturing diversity outside of Norway, which was genetically highly divergent from the Norwegian dragonheads. The historic-modern comparison revealed similar genetic structure in space and limited change through time in Norway. The ENM suggests that dragonhead has not fully achieved its potential distribution in Norway, which is anchored in warmer and drier regions, including areas where it does not occur today. Main conclusions: With the appropriate design procedures, the SNP array technology is promising for genotyping old herbarium specimens; an invaluable source of information from the past. We found no signs of the severe reduction in population size in our temporal genomic data of Norwegian dragonhead. Regardless, the regional populations in Norway are genetically divergent, both from each other and more so from populations outside of Norway, rendering continued protection of all existing populations of the species relevant.

Using Ecological Niche Modelling to Predict Climate Change Responses of Ten Key Fishery Species in Aotearoa New Zealand

<p>The long-term sustainability and security of food sources for an increasing human population will become more challenging as climate change alters growing and harvesting conditions. Significant infrastructure changes could be required to continue to supply food from traditional sources. Fisheries remain the only major protein supply directly harvested from the wild. This likely makes it the most sensitive primary sector to climate change. Overfishing is an additional concern for harvested species. There is a need to anticipate how marine species may respond to climate change to help inform how management might best be prepared for shifting distributions and productivity levels. The most common response of mobile marine species to changes in climate is an alteration of their geographic distributions and/or range shifts. Predicting changes to a species’ range could promote timely development of more sustainable harvest strategies. Additionally, these predictions could reduce potential conflict when different management areas experience increasing or decreasing catches. Ecological Niche Modelling (ENM) is a helpful approach for predicting the response of key fishery species to climate change scenarios. The overall aim of this research was to use the maximum entropy method, Maxent, to perform ENM on 10 commercially important fishery species, managed under the Quota management system in Aotearoa (New Zealand). Occurrence data from trawl surveys were used along with climate layers from Bio-ORACLE to estimate the species niche and then predict distributions in four different future climate scenarios, called Representative Concentration Pathway Scenarios (RCPS), in both 2050 and 2100. With little consensus over the best settings and way to apply the Maxent method, hundreds of variations were tried for each species, and the best model chosen from trial experimentation. In general, Maxent performed well, with evaluation metrics for best models showing little omission error and good discriminatory ability. There was, however, considerable variation between the different species responses to the future climate scenarios. Consistent with other studies, species able to tolerate sub-tropical or temperate conditions tended to expand southward, while subantarctic species generally contracted within their preferred environment. The increasing emissions or ‘business as usual’ climate change scenario consistently presented the most extreme difference from modern predictions. Northern regions of prediction, where sub-tropical or temperate species increased in probability of presence, were often highly uncertain due to novel conditions in future environments. Southern regions were usually less uncertain. Surface temperature consistently influenced base models more so than any other covariates considered, with the exception of bathymetry. Some predictions showed common areas of relative stability, such as hoki and ling on the southern Chatham Rise, potentially indicating future refugia. The preservation of habitats in the putative refugia may be important for long-term fisheries resilience. Furthermore, most species that showed large predicted declines are currently heavily harvested and managed. Overfishing could compound the effects of climate change and put these fisheries at serious risk of collapse. Identification of potential refugial areas could aid strategy adjustments to fishing practice to help preserve stock viability. Additionally, when some species shift, there are areas where new fisheries may emerge. This study offers a perspective of what future distributions could be like under different climate scenarios. The ENM predicts that the ‘business as usual’ scenario, where ‘greenhouse gas’ emissions continue to rise throughout the century, will have a negative impact on multiple aspects of distribution. However, in a reduced emissions scenario, less extreme range shifts are predicted. This study has provided a predictive approach to how fisheries in Aotearoa might change. The next step is to determine whether there is any evidence for the beginning of these changes and to consider how fisheries might best adapt.</p>

Using Ecological Niche Modelling to Predict Climate Change Responses of Ten Key Fishery Species in Aotearoa New Zealand

<p>The long-term sustainability and security of food sources for an increasing human population will become more challenging as climate change alters growing and harvesting conditions. Significant infrastructure changes could be required to continue to supply food from traditional sources. Fisheries remain the only major protein supply directly harvested from the wild. This likely makes it the most sensitive primary sector to climate change. Overfishing is an additional concern for harvested species. There is a need to anticipate how marine species may respond to climate change to help inform how management might best be prepared for shifting distributions and productivity levels. The most common response of mobile marine species to changes in climate is an alteration of their geographic distributions and/or range shifts. Predicting changes to a species’ range could promote timely development of more sustainable harvest strategies. Additionally, these predictions could reduce potential conflict when different management areas experience increasing or decreasing catches. Ecological Niche Modelling (ENM) is a helpful approach for predicting the response of key fishery species to climate change scenarios. The overall aim of this research was to use the maximum entropy method, Maxent, to perform ENM on 10 commercially important fishery species, managed under the Quota management system in Aotearoa (New Zealand). Occurrence data from trawl surveys were used along with climate layers from Bio-ORACLE to estimate the species niche and then predict distributions in four different future climate scenarios, called Representative Concentration Pathway Scenarios (RCPS), in both 2050 and 2100. With little consensus over the best settings and way to apply the Maxent method, hundreds of variations were tried for each species, and the best model chosen from trial experimentation. In general, Maxent performed well, with evaluation metrics for best models showing little omission error and good discriminatory ability. There was, however, considerable variation between the different species responses to the future climate scenarios. Consistent with other studies, species able to tolerate sub-tropical or temperate conditions tended to expand southward, while subantarctic species generally contracted within their preferred environment. The increasing emissions or ‘business as usual’ climate change scenario consistently presented the most extreme difference from modern predictions. Northern regions of prediction, where sub-tropical or temperate species increased in probability of presence, were often highly uncertain due to novel conditions in future environments. Southern regions were usually less uncertain. Surface temperature consistently influenced base models more so than any other covariates considered, with the exception of bathymetry. Some predictions showed common areas of relative stability, such as hoki and ling on the southern Chatham Rise, potentially indicating future refugia. The preservation of habitats in the putative refugia may be important for long-term fisheries resilience. Furthermore, most species that showed large predicted declines are currently heavily harvested and managed. Overfishing could compound the effects of climate change and put these fisheries at serious risk of collapse. Identification of potential refugial areas could aid strategy adjustments to fishing practice to help preserve stock viability. Additionally, when some species shift, there are areas where new fisheries may emerge. This study offers a perspective of what future distributions could be like under different climate scenarios. The ENM predicts that the ‘business as usual’ scenario, where ‘greenhouse gas’ emissions continue to rise throughout the century, will have a negative impact on multiple aspects of distribution. However, in a reduced emissions scenario, less extreme range shifts are predicted. This study has provided a predictive approach to how fisheries in Aotearoa might change. The next step is to determine whether there is any evidence for the beginning of these changes and to consider how fisheries might best adapt.</p>

Modelling potential range expansion of an underutilised food security crop in Sub-Saharan Africa

Despite substantial growth in global agricultural production, food and nutritional insecurity is rising in Sub-Saharan Africa. Identification of underutilised indigenous crops with useful food security traits may provide part of the solution. Enset (Ensete ventricosum) is a perennial banana relative with cultivation restricted to southwestern Ethiopia, where high productivity and harvest flexibility enables it to provide a starch staple for ~20 million people. An extensive wild distribution suggests that a much larger region may be climatically suitable for cultivation. Here we use ensemble ecological niche modelling to predict the potential range for enset cultivation within southern and eastern Africa. We find contemporary bioclimatic suitability for a 12-fold range expansion, equating to 21.9% of crop land and 28.4% of the population in the region. Integration of crop wild relative diversity, which has broader climate tolerance, could enable a 19-fold expansion, particularly to dryer and warmer regions. Whilst climate change may cause a 37% – 52% reduction in potential range by 2070, large centres of suitability remain in the Ethiopian Highlands, Lake Victoria region and the Drakensberg Range. We combine our bioclimatic assessment with socioeconomic data to identify priority areas with high population density, seasonal food deficits and predominantly small-scale subsistence agriculture, where integrating enset may be particularly feasible and deliver climate resilience. When incorporating the genetic potential of wild populations, enset cultivation might prove feasible for an additional 87.2 - 111.5 million people, 27.7 – 33 million of which are in Ethiopia outside of enset’s current cultivation range. Finally, we consider explanations why enset cultivation has not expanded historically, and ethical implications of expanding previously underutilised species.