Population Genomics of New Zealand Pouched Lamprey (kanakana; piharau;Geotria australis)

Abstract

Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft Geotria australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16,000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n=186) and sequence data from Cyt-b (766 bp, n=94) and COI (589 bp, n=20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.

Estimation of effective number of breeders and effective population size in an abundant and heavily exploited marine teleost

“…Our N e estimates are within the range of those reported for marine species exhibiting very large populations (Marandel et al, 2019) for anadromous fishes (Barría et al, 2019;Ferchaud et al, 2016;Miller et al, 2022;Waldman et al, 2019) and elasmobranchs (Dudgeon & Ovenden, 2015;Pazmiño et al, 2017;Reid-Anderson et al, 2019;Venables et al, 2021), and are smaller than those for southern bluefin tuna (Thunnus maccoyii; Waples, Grewe, et al, 2018), albacore tuna (Thunnus alalunga; Laconcha et al, 2015) and New Zealand hoki (Macruronus novaezelanidae; Koot et al, 2021), which support far more productive fisheries than snapper. Although fewer studies have explored N b in marine species, due to the close relationship…”

“…Our N e estimates are within the range of those reported for marine species exhibiting very large populations (Marandel et al., 2019 ), and are similar to N e estimates generated for species with reproductive strategies comparable to snapper, including the giant black tiger shrimp ( Penaeus monodon ; Vu et al., 2020 ), Sydney rock oyster ( Saccostrea glomerata ; O'Hare et al., 2021 ), green abalone ( Haliotis fulgens ; Gruenthal et al., 2014 ), Pacific cod ( Gadus macrocephalus ; Suda et al., 2017 ), white hake ( Urophycis tenuis ; Roy et al., 2012 ), and redbelly yellowtail fusilier ( Caesio cuning ; Ackiss et al., 2018 ). As expected, the two snapper N e estimates are generally larger than those for anadromous fishes (Barría et al., 2019 ; Ferchaud et al., 2016 ; Miller et al., 2022 ; Waldman et al., 2019 ) and elasmobranchs (Dudgeon & Ovenden, 2015 ; Pazmiño et al., 2017 ; Reid‐Anderson et al., 2019 ; Venables et al., 2021 ), and are smaller than those for southern bluefin tuna ( Thunnus maccoyii ; Waples, Grewe, et al., 2018 ), albacore tuna ( Thunnus alalunga ; Laconcha et al., 2015 ) and New Zealand hoki ( Macruronus novaezelanidae ; Koot et al., 2021 ), which support far more productive fisheries than snapper. Although fewer studies have explored N b in marine species, due to the close relationship between N e and N b , similar trends to those described above occur between our results and similar studies with regard to N b (Davenport et al., 2021 ; King et al., 2023 ; Puritz et al., 2016 ; Waples, Grewe, et al., 2018 ; Whiteley et al., 2015 ).…”

Estimation of effective population size and effective number of breeders in an abundant and heavily exploited marine teleost

“…As expected, the two snapper N e estimates are generally larger than those for anadromous fishes Our N e estimates are within the range of those reported for marine species exhibiting very large populations (Marandel et al 2019), and are similar to N e estimates generated for species with reproductive strategies comparable to snapper, including the giant black tiger shrimp (Penaeus monodon; Vu et al 2020), Sydney rock oyster (Saccostrea glomerata; O 'Hare et al 2021), green abalone (Haliotis fulgens; Gruenthal et al 2014), Pacific cod (Gadus macrocephalus; Suda et al 2017), white hake (Urophycis tenuis; Roy et al 2012) and redbelly yellowtail fusilier (Caesio cuning; Ackiss et al 2018). As expected, the two snapper N e estimates are generally larger than those for anadromous fishes (Ferchaud et al 2016, Barría et al 2019, Waldman et al 2019, Miller et al 2022) and elasmobranchs (Dudgeon and Ovenden 2015, Pazmiño et al 2017, Reid-Anderson et al 2019, Venables et al 2021, and are smaller than those for southern bluefin tuna (Thunnus maccoyii; Waples et al 2018a), albacore tuna and New Zealand hoki (Macruronus novaezelanidae; Koot et al 2021), which support far more productive fisheries than snapper.…”

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

“… 29 , 30 These species are part of a recently diverged clade that last shared a common ancestor approximately 12–13 million years ago (mya; roughly equivalent to human/orangutan divergence) 31 – 33 and that shared a common ancestor with Petromyzon approximately 30 mya. Other lamprey species that have not been fully assembled thus far include members of the genera Geotria (a draft assembly is available) 34 and Mordacia , which are found in the Southern hemisphere and diverged from the common ancestor of Petromyzon and other Northern hemisphere species ~200 mya. 21 , 31 …”