A comparison of genetic and genomic approaches to represent evolutionary potential in conservation planning

Journal of Biogeography

Beger

Henriques

et al. 2021

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Aim Intraspecific diversity is a significant component of adaptive potential, and thus, it is important to identify the evolutionary processes that have and will continue to shape the molecular diversity of natural populations. This study aims to untangle the possible drivers of intraspecific molecular diversity by testing whether patterns of historical climatic stability or contemporary range position correlate with molecular diversity. Location South African coastline. Taxa The cape urchin (Parechinus angulosus), common shore crab (Cyclograpsus punctatus) and granular limpet (Scutellastra granularis). Methods Species distributions were hindcasted to the Last Glacial Maximum to assess the biogeography of the study species. Linear models were built to compare the relationships between historical climatic stability or contemporary distributional ranges with extant genetic (mtDNA) and genomic (SNP) diversity. Results We found large differences in the historical ranges among species and time periods. Regions of higher habitat stability corresponded to regions of higher molecular diversity, but historical climatic variability was not a predictor of molecular diversity within linear models. Lower genetic diversity values, and higher genetic differentiation, were detected in edge populations, but this was not consistent across marker type or species. Main conclusions Both historical and contemporary processes are potentially driving patterns of diversity, but a large portion of the variation in molecular diversity remains unexplained. Our findings suggest that marine species within cool‐temperate bioregions in the Southern Hemisphere may have more complex biogeographic and evolutionary histories than terrestrial taxa and/or coastal species within northern, formerly glaciated regions.

Section: Methodsmentioning

confidence: 99%

Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species

Journal of Biogeography

Beger

Henriques

et al. 2021

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“…The South African coastline encompasses a large variety of ecosystems, including rocky and sandy shores, kelp forests, estuaries and coral reefs, as well as contrasting environmental conditions (Branch & Branch, 2018) that drive high levels of coastal marine biodiversity. Four major phylogeographic breaks have been identified, and most coastal species, including organisms with high dispersal capacities, are divided into genetic lineages whose distributional ranges broadly match the bioregions (Figure 1; Teske et al, 2011; Wright et al, 2015), with evidence for temperature and salinity as important drivers of potential local adaptation (Nielsen et al, 2020; Phair et al, 2019; Teske et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition

Dalongeville

Diversity and Distributions

Teske

et al. 2022

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Aim: Intraspecific genetic variation is a key component of biodiversity, with higher diversity indicating greater resilience and population substructuring suggesting unique evolutionary histories. Comparative approaches, in which intraspecific genetic variation is assessed across multiple species, are powerful tools to identify evolutionary hotspots, but are still rarely applied at spatial scales relevant to conservation planning.Here, we use comparative phylogeography to understand patterns and potential drivers of genetic variation within a biodiversity and ocean warming hotspot. Location:The South African coastline, Indian/Atlantic Oceans. Methods:A literature search was conducted to obtain mitochondrial DNA cytochrome oxidase c subunit I and cytochrome b sequence data for 17 marine fish and invertebrate species. From these data, we compared averages of haplotype and nucleotide diversity, and within-region Φ ST between four biogeographic provinces in the region.Mixed linear models tested whether environmental variability, habitat preference, or geographic location significantly influence genetic variation. Results:Average diversity values differed between haplotype and nucleotide diversity, but both broadly displayed highest diversity levels within the South-West bioregion, which is also a region of high levels of within-region Φ ST . Range in sea surface temperatures (SSTs) was the only significant fixed-effect term in the haplotype diversity mixed linear models. Mean SST, stability in SSTs since the Mid-Holocene and position within the species' geographic distribution all had no significant effect on genetic variation. Main conclusions:Along this coastline characterized by high environmental heterogeneity, we find that variation in temperature is a prominent source of intraspecific variation. Genetic diversity differs between bioregions, but does not display higher levels within the core of each species' range when assessed across multiple species. With elevated levels of genetic diversity, the South-West region of the South African coast is highlighted as a conservation priority area, representing both high genetic diversity and differentiation across taxa.

“…However, most assessments of species range shifts from SDMs disregard the occurrence of intraspecific climatic tolerances, local adaptation, and gene flow (Rilov et al, 2019). This is problematic, as genetic variation is a crucial component of a species’ resilience, with areas of high neutral diversity inferring more raw material for adaptation to occur, and high adaptive diversity inferring pre‐adapted populations (Bitter et al, 2019; Nielsen, Beger, et al, 2020). There have been efforts to assess lineage (D’Amen et al, 2013; Espíndola et al, 2012) and population‐level (Banta et al, 2012; Jay et al, 2012) responses to climate change with ‘genetic SDMs’, often showing a disproportionate loss of genetic variation over the species’ range.…”

Section: Introductionmentioning

confidence: 99%

Distinct interspecific and intraspecific vulnerability of coastal species to global change

Henriques

Beger

et al. 2021

Global Change Biology

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Characterising and predicting species responses to anthropogenic global change is one of the key challenges in contemporary ecology and conservation. The sensitivity of marine species to climate change is increasingly being described with forecasted species distributions, yet these rarely account for population level processes such as genomic variation and local adaptation. This study compares inter‐ and intraspecific patterns of biological composition to determine how vulnerability to climate change, and its environmental drivers, vary across species and populations. We compare species trajectories for three ecologically important southern African marine invertebrates at two time points in the future, both at the species level, with correlative species distribution models, and at the population level, with gradient forest models. Reported range shifts are species‐specific and include both predicted range gains and losses. Forecasted species responses to climate change are strongly influenced by changes in a suite of environmental variables, from sea surface salinity and sea surface temperature, to minimum air temperature. Our results further suggest a mismatch between future habitat suitability (where species can remain in their ecological niche) and genomic vulnerability (where populations retain their genomic composition), highlighting the inter‐ and intraspecific variability in species’ sensitivity to global change. Overall, this study demonstrates the importance of considering species and population level climatic vulnerability when proactively managing coastal marine ecosystems in the Anthropocene.