Advancing Biogeography Through Population Genomics

Johnson, Jeremy S.; Krutovsky, Konstantin V.; Rajora, Om P.; Gaddis, Keith D.; Cairns, David M.

doi:10.1007/13836_2018_39

Cited by 11 publications

(7 citation statements)

References 226 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, future studies are encouraged to include other drivers important for observed biogeography of plants and animals, such as seasonality, climate zones and geographical regions, at multiple time points in sampling strategy for comprehensive conclusions. A population ecology approach could be further applied to improve the methodology by evaluating genome legacies from a biological evolutionary perspective [79].…”

Section: Resultsmentioning

confidence: 99%

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Wang

Sun

et al. 2020

The ISME Journal

View full text Add to dashboard Cite

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

show abstract

Section: Resultsmentioning

confidence: 99%

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Wang

Sun

et al. 2020

The ISME Journal

View full text Add to dashboard Cite

show abstract

“…Hu et al explored the key drivers of biological community and found that MAT had the strongest influence on bacterial communities [57]. In addition, geological processes may lead to the biological speciation and evolution [59,60]. Poltak et al proposed an evolutionary scenario, in which the common ancestor of Archaea harbored the ability for methane metabolism (including the evolution of methyl-coenzyme M reductasecontaining hot spring Archaea) [61,62].…”

Section: Discussionmentioning

confidence: 99%

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Liu

Jiao

et al. 2021

Microbiome

View full text Add to dashboard Cite

Background Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. Results The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. Conclusions These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions.

show abstract

“…The first 256 genome skims of the PhyloNorway dataset were used in an ancient DNA study from southern Sweden, and greatly enhanced the ability to taxonomically assign the sequences [60]. Furthermore, it may enable studies of population genomics based on herbarium material [61] or sediment samples, as has been done for algae [62] and humans [63].…”

Section: Utilisation Of the Genome Skimming Datamentioning

confidence: 99%

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Alsos

Lavergne

Merkel

et al. 2020

Plants

104

View full text Add to dashboard Cite

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

show abstract

Advancing Biogeography Through Population Genomics

Cited by 11 publications

References 226 publications

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Contact Info

Product

Resources

About