De novo SNP discovery and strong genetic structuring between upstream and downstream populations of Paratya australiensis Kemp, 1917 (Decapoda: Caridea: Atyidae)

Rahman, Sharmeen; Schmidt, Daniel J.; Hughes, Jane

doi:10.1093/jcbiol/rux117

Cited by 3 publications

(4 citation statements)

References 37 publications

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Section: Local Genetic Diversitycontrasting

confidence: 79%

“…Diversity metrics (e.g., H e ) varied among sampling sites, but were generally lower compared to a previous study on a confamilial shrimp species using similar markers (Rahman et al 2018) sampled in Eastern Australia across 15 km distance. However, the Green Valley watershed displayed exceptionally high genetic diversity consistent with the results from Rahman et al (2018). The higher genetic diversity in Green Valley watershed is somewhat intriguing and we hypothesize that it could result from either (i) this watershed may have been a refugium during glaciation periods and maintains more ancestral polymorphisms than recently colonized watersheds, and/or (ii) the Green Valley watershed may have a larger current effective population size.…”

Section: Local Genetic Diversitycontrasting

confidence: 79%

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Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): watershed and stream networks define gene pool boundaries

Ada,

Vandergast,

Fisher

et al. 2024

Conserv Genet

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Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica. Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, FST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, FST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (Ne = 62.4–147.1). Genetic diversity was variable across sites and watersheds (He = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity.

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Section: Local Genetic Diversitycontrasting

confidence: 79%

Section: Local Genetic Diversitycontrasting

confidence: 79%

Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): watershed and stream networks define gene pool boundaries

Ada,

Vandergast,

Fisher

et al. 2024

Conserv Genet

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show abstract

“…This was in order to confirm the mtDNA lineage to which they belonged. Details of the barcoding of Booloumba Creek individuals is described in Rahman, Schmidt & Hughes (2018).…”

Section: Mtdna Barcoding and Phylogenetic Analysis Of Booloumba Creekmentioning

confidence: 99%

“…Such strong structure could be explained by the presence of different lineages (or cryptic species) occur in the two BOH and BOL populations. However, the phylogenetic analysis based on a fragment of the mitochondrial COI gene showed that the individuals from high and low elevation populations were from the same lineage (4) (Rahman, Schmidt & Hughes, 2018).…”

Section: Population Divergencementioning

confidence: 99%

Genetic structure of Australian glass shrimp,Paratya australiensis,in relation to altitude

Rahman

Schmidt

Hughes

2020

PeerJ

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Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.

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Spatial sorting caused by downstream dispersal: implication for morphological evolution in isolated populations of fat minnow inhabiting small streams flowing through terraced rice paddies

Yamada

2024

Journal of Evolutionary Biology

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The evolutionary forces arising from differential dispersal are known as “spatial sorting,” distinguishing them from natural selection arising from differential survival or differential reproductive success. Spatial sorting is often considered to be transient because it is offset by the return of dispersers in many cases. However, in riverine systems, spatial sorting by downstream dispersal can be cumulative in habitats upstream of migration barriers such as weirs or falls, which can block the return of the dispersers. Terraced rice paddies are often found on steep mountain slopes in Japan and often incorporate small streams with numerous migration barriers. This study investigated the morphological features of fat minnow, Rhynchocypris oxycephalus jouyi (Cyprinidae), inhabiting above-barrier habitats of the small streams flowing through flood-prone terraced rice paddies and examined their function via a mark–recapture experiment. Although this study did not reveal a consistent pattern across all local populations, some above-barrier populations were characterized by individuals with a thinner caudal peduncle, thinner body, and longer ventral caudal fin lobes than those in neighbouring mainstream populations. A mark–recapture experiment during minor flooding showed that a thinner caudal peduncle and deeper body helped fat minnow avoid downstream dispersal and ascend a small step, and suggested that a longer ventral caudal fin lobe was important for ascending. These results suggest that the caudal morphologies of some above-barrier populations avoid or reduce the risk of downstream dispersal, supporting the idea that spatial sorting shapes functional traits, enhancing the spatial persistence of individuals in upstream habitats.

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De novo SNP discovery and strong genetic structuring between upstream and downstream populations of Paratya australiensis Kemp, 1917 (Decapoda: Caridea: Atyidae)

Cited by 3 publications

References 37 publications

Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): watershed and stream networks define gene pool boundaries

Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): watershed and stream networks define gene pool boundaries

Genetic structure of Australian glass shrimp,Paratya australiensis,in relation to altitude

Spatial sorting caused by downstream dispersal: implication for morphological evolution in isolated populations of fat minnow inhabiting small streams flowing through terraced rice paddies

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