scholarly journals Coalescent times, life history traits and conservation concerns: an example from four shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescent pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Shallow seamounts represent speciation islands for circumglobal yellowtail Seriola lalandi

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sven Kerwath ◽  
Rouvay Roodt-Wilding ◽  
Toufiek Samaai ◽  
Henning Winker ◽  
Wendy West ◽  
...  
Keyword(s):  
Life History ◽  
Genetic Structure ◽  
Southern Africa ◽  
Life History Traits ◽  
Population Connectivity ◽  
Shark Species ◽  
Heterogeneous Environments ◽  
Genetic Structuring ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

AbstractPhenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shallow oceanic seamounts are known aggregation sites for pelagic species, but their role in genetic structuring of widely distributed species remains poorly understood. The yellowtail kingfish (Seriola lalandi), a commercially valuable, circumglobal, epipelagic fish species occurs in two genetically distinct Southern Hemisphere populations (South Pacific and southern Africa) with low levels of gene-flow between the regions. Two shallow oceanic seamounts exist in the ocean basins around southern Africa; Vema and Walters Shoal in the Atlantic and Indian oceans, respectively. We analysed rare samples from these remote locations and from the South African continental shelf to assess genetic structure and population connectivity in S. lalandi and investigated life-history traits by comparing diet, age, growth and maturation among the three sites. The results suggest that yellowtail from South Africa and the two seamounts are genetically and phenotypically distinct. Rather than mere feeding oases, we postulate that these seamounts represent islands of breeding populations with site-specific adaptations.

scholarly journals Ocean-wide genomic variation in Gray's beaked whales, Mesoplodon grayi

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
M. V. Westbury ◽  
K. F. Thompson ◽  
M. Louis ◽  
A. A. Cabrera ◽  
M. Skovrind ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
South Australia ◽  
Population Connectivity ◽  
Genomic Variation ◽  
Suitable Habitat ◽  
Effective Population ◽  
Beaked Whales ◽  
Marine Megafauna ◽  
Demographic Patterns

The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale ( Mesoplodon grayi ) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa ( n = 2) and South Australia ( n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.

scholarly journals Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

2020 ◽  
Author(s):  
Tlou Caswell Chokoe ◽  
Khanyi Hadebe ◽  
Farai Muchadeyi ◽  
Khathutshelo Nephawe ◽  
Edgar Dzomba ◽  
...  
Keyword(s):  
Negative Impact ◽  
Demographic History ◽  
Conservation Status ◽  
Snp Marker ◽  
Conservation Strategies ◽  
Effective Population ◽  
North West ◽  
Genome Wide ◽  
A Genome ◽  
Indigenous Goat

Abstract Background: Indigenous goats forms the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Results: Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and 41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH >5Mb) was highest in FS (0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN) to 98.05Mb (GP and NW). Distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were >5Mb in length than the other categories. Assuming two hypothetical ancestral populations, the population from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP shared an origin but have substantial admixture from the EC and NW populations.Conclusions: These findings indicated a greater negative impact of inbreeding in recent times which is important for planning conservation strategies. It was revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at different recent and ancient events when a genome-wide SNP marker was used.

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