The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes

The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.     

Biodiversity,biogeography, and connectivity of polychaetes in the world's largest marine minerals exploration frontier

Aim

The abyssal Clarion-Clipperton Zone (CCZ), Pacific Ocean, is an area of commercial importance owing to the growing interest in mining high-grade polymetallic nodules at the seafloor for battery metals. Research into the spatial patterns of faunal diversity, composition, and population connectivity is needed to better understand the ecological impacts of potential resource extraction. Here, a DNA taxonomy approach is used to investigate regional-scale patterns of taxonomic and phylogenetic alpha and beta diversity, and genetic connectivity, of the dominant macrofaunal group (annelids) across a 6 million km² region of the abyssal seafloor.

Location

The abyssal seafloor (3932–5055 m depth) of the Clarion-Clipperton Zone, equatorial Pacific Ocean.

Methods

We used a combination of new and published barcode data to study 1866 polychaete specimens using molecular species delimitation. Both phylogenetic and taxonomic alpha and beta diversity metrics were used to analyse spatial patterns of biodiversity. Connectivity analyses were based on haplotype distributions for a subset of the studied taxa.

Results

DNA taxonomy identified 291–314 polychaete species from the COI and 16S datasets respectively. Taxonomic and phylogenetic beta diversity between sites were relatively high and mostly explained by lineage turnover. Over half of pairwise comparisons were more phylogenetically distinct than expected based on their taxonomic diversity. Connectivity analyses in abundant, broadly distributed taxa suggest an absence of genetic structuring driven by geographical location.

Main Conclusions

Species diversity in abyssal Pacific polychaetes is high relative to other deep-sea regions. Results suggest that environmental filtering, where the environment selects against certain species, may play a significant role in regulating spatial patterns of biodiversity in the CCZ. A core group of widespread species have diverse haplotypes but are well connected over broad distances. Our data suggest that the high environmental and faunal heterogeneity of the CCZ should be considered in future policy decisions.     

Integrating carbon stocks and landscape connectivity for nature-based climate solutions

Actions to protect against biodiversity loss and climate change will require a framework that addresses synergies between these interrelated issues. In this study, we present methods for identifying areas important for the implementation of nature-based climate solutions and biodiversity conservation by intersecting high-resolution spatial data for carbon storage and landscape connectivity. We explored the spatial congruence of carbon and connectivity in Ontario, Canada and examined effectiveness of current protected areas coverage. We found a weak positive relationship between carbon stocks and landscape connectivity; however, our maps revealed large hotspots, with high values of both indices, throughout the boreal forest and northern peatlands and smaller, isolated hotspots, in the settled landscapes of the south. Location of hotspots varied depending on whether we considered forest or soil carbon. Further, our results show that current protected and conserved areas in Ontario only cover 13% of landscapes with the highest values for both carbon storage and connectivity. Protection or restoration of areas that maximize the co-benefits of carbon storage and connectivity would make significant contributions toward ambitious national targets to reduce greenhouse gas emissions and conserve biodiversity.     

Geoclimatic factors influence the population genetic connectivity of Incarvillea arguta (Bignoniaceae) in the Himalaya–Hengduan Mountains biodiversity hotspot

Geoclimatic factors related to the uplift of the Himalaya and the Quaternary climatic oscillations influence the population genetic connectivity in the Himalaya–Hengduan Mountains (HHM) biodiversity hotspot. Therefore, to explore the relative roles played by these two factors, we examined the population dynamics and dispersal corridors of Incarvillea arguta (Royle) Royle incorporating ensemble species distribution modelling (SDM). Thirty‐seven populations were genotyped using plastid chloroplast DNA and low copy nuclear gene (ncpGS) sequences. Phylogeographic analysis was carried out to reveal the genetic structure and lineage differentiation. Ensemble SDMs were carried out for distributional change in the last glacial maximum, present, and future. Finally, the least cost path method was used to trace out possible dispersal corridors. The haplotypes were divided into four clades with strong geographical structure. The late Miocene origin of I. arguta in the western Himalaya ca. 7.92 Ma indicates lineage diversification related to the uplift of the HHM. The variability in habitat connectivity revealed by SDM is due to change in suitability since the Pleistocene. A putative dispersal corridor was detected along the drainage systems and river valleys, with strong support in the eastern Hengduan Mountains group. Our results support the signature of geoclimatic influence on population genetic connectivity of I. arguta in the HHM. We proposed that the major drainage systems might have assisted the rapid dispersal of isolated riverine plant species I. arguta in the HHM. The population genetic connectivity, using the fine‐tuned ensemble SDMs, enables scientists and policymakers to develop conservation strategies for the species gene pool in the HHM biodiversity hotspots.     

Is realised connectivity among populations of aquatic fauna predictable from potential connectivity?

1. Effective management of aquatic fauna requires knowledge of the ways in which populations in different catchments and sub‐catchments are connected. A powerful way to estimate this is using genetic markers, which provide information on the average amount of genetic connectivity among populations over generations. Although many studies of genetic connectivity have appeared in the literature, there are innumerable species that have not been studied. 2. This study explores whether it is possible to make broad generalisations about population connectivity, based on readily available information in the form of species life history and architecture of the aquatic habitat. 3. A number of models have been proposed to explain the pattern of connectivity shown by aquatic species with different life‐history characteristics, for example, the stream hierarchy model, Isolation by Distance, the Death Valley Model, the headwater model and panmixia. 4. In this study, we propose a dichotomous key to assign species to different models of potential connectivity. The key is based on a few very simple questions about the life history of the species and the geographical arrangement of study sites. We then assessed the performance of the key with 109 data sets of Australian fish and macroinvertebrates, using genetic data to provide an estimate of realised connectivity. 5. The realised connectivity fitted the proposed potential connectivity model in over 70% of cases, and we suggest this might be a useful initial approach for managers where empirical data are lacking.     

The distribution and cellular origin of vasoactive intestinal polypeptide in the avian gastrointestinal tract and pancreas

Summary The distribution and origins of vasoactive intestinal peptide (VIP) in the gut and pancreas of the turkey were studied by radioimmunoassay of tissue extracts and by immunocytochemistry. Several antisera were used that vary in their specificity for different regions of porcine or chicken VIP. Radioimmunoassays using NH₂-terminal specific antisera that react almost equally with porcine and chicken VIP's revealed significant amounts of immunoreactive VIP in extracts of pancreas, brain and all regions of the gastrointestinal tract from crop to colon. Highest concentrations (300pmol/g) were found in the colon muscle, and concentrations were generally low (< 20 pmol/g) in the mucosal layers of the small intestine. After ion exchange chromatography of extracts on CM-Sephadex three immunoreactive forms of VIP were separated corresponding to the three molecular forms previously found in mammalian gut extracts. In immunocytochemical studies nerve fibres were found throughout the gut, and in the pancreas. Immunoreactive nerve cell bodies were also identified in the submucous plexus throughout the gut, but were particularly prominent in the oesophagus and pancreas. It has previously been shown that VIP is a strong stimulant of the flow of pancreatic juice in birds whereas the structurally related hormone secretin, which is known to control the flow of pancreatic juice in mammals, is a weak stimulant. It is proposed that in birds VIP might regulate the pancreas, and other aspects of gut function, as a neurotransmitter or neurohormone.     

Crosstalk between translation and the aggresome–autophagy pathway

Many neurodegenerative disorders feature the presence of misfolded polypeptide-containing intracellular inclusion bodies biochemically and morphologically analogous to cellular aggresomes. However, it is largely unknown how misfolded polypeptides form aggresomes and are eventually cleared by the aggresome-macroautophagy/autophagy pathway, so-called aggrephagy. Our recent study revealed that when the ubiquitin-proteasome system is impaired, the accumulated misfolded polypeptides are selectively recognized and transported to the aggresome by a CED complex. This complex is composed of CTIF, originally identified as a specific factor for nuclear cap-binding protein complex (a heterodimer of NCBP1/CBP80 and NCBP2/CBP20)-dependent translation (CT), and its associated factors EEF1A1 and DCTN1. Aggresomal targeting of a misfolded polypeptide via the CED complex is accompanied by CTIF release from the CT complex and thereby inhibits CT efficiency. Therefore, our study provides new mechanistic insights into the crosstalk between translational inhibition and aggresome formation under the influence of a misfolded polypeptide.     

Are all data types and connectivity models created equal? Validating common connectivity approaches with dispersal data

Aim

There is enormous interest in applying connectivity modelling to resistance surfaces for identifying corridors for conservation action. However, the multiple analytical approaches used to estimate resistance surfaces and predict connectivity across resistance surfaces have not been rigorously compared, and it is unclear what methods provide the best inferences about population connectivity. Using a large empirical data set on puma (Puma concolor), we are the first to compare several of the most common approaches for estimating resistance and modelling connectivity and validate them with dispersal data.

Location

Southern California, USA.

Methods

We estimate resistance using presence‐only data, GPS telemetry data from puma home ranges and genetic data using a variety of analytical methods. We model connectivity with cost distance and circuit theory algorithms. We then measure the ability of each data type and connectivity algorithm to capture GPS telemetry points of dispersing pumas.

Results

We found that resource selection functions based on GPS telemetry points and paths outperformed species distribution models when applied using cost distance connectivity algorithms. Point and path selection functions were not statistically different in their performance, but point selection functions were more sensitive to the transformation used to convert relative probability of use to resistance. Point and path selection functions and landscape genetics outperformed other methods when applied with cost distance; no methods outperformed one another with circuit theory.

Main conclusions

We conclude that path or point selection functions, or landscape genetic models, should be used to estimate landscape resistance for wildlife. In cases where resource limitations prohibit the collection of GPS collar or genetic data, our results suggest that species distribution models, while weaker, may still be sufficient for resistance estimation. We recommend the use of cost distance‐based approaches, such as least‐cost corridors and resistant kernels, for estimating connectivity and identifying functional corridors for terrestrial wildlife.