The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast

Brielle, Esther S.; Fleisher, Jeffrey; Wynne‐Jones, Stephanie; Broomandskhoshbacht, Nasreen; Callan, Kim; Curtis, Elizabeth; Iliev, Lora; Lawson, Ann Marie; Oppenheimer, Jonas; Qiu, Lijun; Stewardson, Kristin; Workman, Noah; Zalzala, Fatma; Ayodo, George; Gidna, Agness; Kabiru, Angela; Kwekason, Amandus; Mabulla, Audax; Manthi, Fredrick K.; Ndiema, Emmanuel; Ogola, Christine; Sawchuk, Elizabeth A.; Ali, Bassam R.; Ben-Salem, Salma; Letellier, Thierry; Pierron, Denis; Radimilahy, Chantal; Rakotoarisoa, Jean-Aimé; Culleton, Brendan J.; Mallick, Swapan; Rohland, Nadin; Patterson, Nick; Mwenje, Mohammed Ali; Ahmed, Khalfan Bini; Mohamed, Mohamed Mchulla; Williams, Sloan R.; Monge, Janet; Kusimba, Sibel; Prendergast, Mary E.; Reich, David; Kusimba, Chapurukha M.

doi:10.1101/2022.07.10.499442

Cited by 4 publications

(4 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Critical sources of information that need to be elevated are the perspectives and knowledge of indigenous voices that have long term observational records and environmental stewardship. Examples include the recent report that oral traditions of the people from the Swahili coast resolved long‐standing questions about the origins of its people (Brielle et al 2023); and key insights into aquatic systems obtained from mātauranga Māori (encompassing not only Māori knowledge, but also Māori culture, values and worldview; Hikuroa 2017), which have led to sustainable management practices across both freshwater (Kusabs and Quinn 2009) and marine environments (Paul‐Burke et al 2018).…”

Section: The Power Of Time Series Data and Analysismentioning

confidence: 99%

Cascading, interactive, and indirect effects of climate change on aquatic communities, habitats, and ecosystems

Menden‐Deuer

Mullarney

Boersma

et al. 2023

Limnology & Oceanography

View full text Add to dashboard Cite

Climate-change is rapidly and intensively altering aquatic communities and habitats. While previous work has focused on direct effects of potential drivers, indirect and interactive effects on organisms and ecosystems have received less attention. Here, we give an overview of contributions to a special issue in Limnology and Oceanography that addresses this knowledge gap. Contributions covered diverse habitats, from polar to tropical regions, alpine streams to coral reefs. Several studies relied on time-series to identify indirect effects, thus emphasizing our need to maintain high-quality time-series data. Time-series are particularly crucial now that the pace of climate-change on aquatic-ecosystems is accelerating. Another common theme is the role of speciesspecific characteristics in physiology, behavior or genetics in aquatic ecosystem function. The addition of interand intra-specific variability to investigations of climate-change may be challenging particularly since ecosystem studies typically involve a large parameter space of environmental and biological variables across spatial and temporal scales. However, the results demonstrate that inclusion of species-specific dynamics, although challenging, can deliver mechanistic insights into aquatic ecosystem patterns and processes. Some contributions leverage habitat changes from disturbances or climate shifts to document capacity for resilience or recovery of pelagic and benthic communities. Jointly, the results in this special issue document fruitful approaches and provide urgent information needed for deciphering aquatic ecosystem responses to climate forcings. This information is foundational if we wish to tackle the combined effects of climate change and other human impacts with maximum efficacy and minimize unintended consequences for biodiversity and ecosystem functioning. MotivationClimate change is rapidly altering aquatic ecosystems on unprecedented scales. Climate-related environmental impacts altering freshwater and coastal habitats often exacerbate other human-induced stressors that negatively affect organisms and ecosystem function, such as urbanization, and persistent pollutants that have permeated the biosphere from freshwater systems to the deep sea. These impacts put species and ecosystems at risk and ultimately endanger humanity's intricate dependence on aquatic ecosystems. These threats also highlight the urgent need to gain mechanistic insights and to improve predictions of how climate change affects aquatic organisms, community structure, and ecosystem function, both now and in future conditions. However, quantifying and predicting the effects of climate change and other human impacts on aquatic organisms remains a major and pressing challenge. Insight into feedbacks and indirect and interactive effects have often been limited by data availability since

show abstract

Section: The Power Of Time Series Data and Analysismentioning

confidence: 99%

Cascading, interactive, and indirect effects of climate change on aquatic communities, habitats, and ecosystems

Menden‐Deuer

Mullarney

Boersma

et al. 2023

Limnology & Oceanography

View full text Add to dashboard Cite

show abstract

“…The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 8 , PRJEB51180 (ENA) 9 , PRJCA005576 (GSA) 10 , PRJEB52849 (ENA) 11 , PRJEB42656 (ENA) 12 , PRJEB52230 (ENA) 13 , PRJNA786530 (SRA) 14 , PRJNA1005336 (SRA) 15 , PRJEB51440 (ENA) 16 , PRJEB56773 (ENA) 17 , PRJEB49291 (ENA) 18 , PRJEB42781 (ENA) 19 , PRJEB46734 (ENA) 20 , PRJNA798381 (SRA) 21 , PRJEB42269 (ENA) 22 , PRJEB47891 (ENA) 23 , PRJEB54899 (ENA) 24 , PRJEB43715 (ENA) 25 , PRJEB39134 (ENA) 26 , PRJEB46162 (ENA) 27 , PRJEB46875 (ENA) 28 , PRJEB44430 (ENA) 29 , PRJEB42199 (ENA) 30 , PRJEB38555 (ENA) 31 , PRJEB55327 (ENA) 32 , PRJEB56213 (ENA) 33 , PRJEB51862 (ENA) 34 , PRJEB58698 (ENA) 35 , PRJEB62503 (ENA) 36 , PRJEB66319 (ENA) 37 , PRJEB59008 (ENA) 38 , PRJEB61818 (ENA) 39 , PRJEB50368 (ENA) 40 , PRJEB50857 (ENA) 41 , PRJCA003870 (GSA) 42 , PRJCA003699 (GSA) 43 , PRJEB53475 (ENA) 44 , PRJEB37782 (ENA) 45 , PRJNA687817 (SRA) 46 , PRJEB42372 (ENA) 47 , PRJEB66422 (ENA) 48 , PRJEB57364 (ENA) 49 .…”

Section: Data Availabilitymentioning

confidence: 99%

Improving data archiving practices in ancient genomics

Bergström

2023

Preprint

View full text Add to dashboard Cite

The sequencing of ancient DNA from preserved biological remains is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is made available in public archives in an appropriate fashion, its long-term value will not be fully realised. I surveyed publicly archived data from 28 recent ancient genomics studies. I found that half of the studies archived incomplete subsets of the generated genomic data, preventing accurate replication and representing a loss of data of potential use for future research. None of the studies met all archiving criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: 1) archive all sequencing reads, not just those that can be aligned to a reference genome, 2) archive read alignments as well, but as secondary analysis files linked to the underlying raw read files, 3) provide correct experiment metadata on how samples, libraries and sequencing runs relate to each other, 4) provide informative sample metadata in the public archives, 5) publish and archive data from screening, low-coverage, poorly performing and negative experiments, and 6) review data archiving as part of peer review processes. Given the reliance on destructive sampling of finite material, I argue that ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

show abstract

“…Bringing evidence of environmental and climatic changes into discourse for understanding human history and behavior is not new ( 1 ). However, recent years have seen more concerted efforts to promote consilience through dialogue between the sciences and humanities ( 2 , 3 ), as well as the application of genetics to questions of past human geography and demography ( 4 , 5 ). Such studies are generally published in scientific journals ( 6 – 9 ), arguably limiting their influence on historians for whom monographs and a small number of history journals remain vital academic currency ( 10 – 13 ).…”

Section: Introductionmentioning

confidence: 99%

The dahliagram: An interdisciplinary tool for investigation, visualization, and communication of past human-environmental interaction

Frachetti,

Di Cosmo,

Esper

et al. 2023

Sci. Adv.

View full text Add to dashboard Cite

Investigation into the nexus of human-environmental behavior has seen increasing collaboration of archaeologists, historians, and paleo-scientists. However, many studies still lack interdisciplinarity and overlook incompatibilities in spatiotemporal scaling of environmental and societal data and their uncertainties. Here, we argue for a strengthened commitment to collaborative work and introduce the “dahliagram” as a tool to analyze and visualize quantitative and qualitative knowledge from diverse disciplinary sources and epistemological backgrounds. On the basis of regional cases of past human mobility in eastern Africa, Inner Eurasia, and the North Atlantic, we develop three dahliagrams that illustrate pull and push factors underlying key phases of population movement across different geographical scales and over contrasting periods of time since the end of the last Ice Age. Agnostic to analytical units, dahliagrams offer an effective tool for interdisciplinary investigation, visualization, and communication of complex human-environmental interactions at a diversity of spatiotemporal scales.

show abstract

The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast

Cited by 4 publications

References 69 publications

Cascading, interactive, and indirect effects of climate change on aquatic communities, habitats, and ecosystems

Cascading, interactive, and indirect effects of climate change on aquatic communities, habitats, and ecosystems

Improving data archiving practices in ancient genomics

The dahliagram: An interdisciplinary tool for investigation, visualization, and communication of past human-environmental interaction

Contact Info

Product

Resources

About