Integration of ecology,demography and genetics to reveal population structure and persistence: a mini review and case study of stream‐dwelling Dolly Varden

Abstract – Spatial structures can drive population dynamics and persistence. The roles of space and dispersal on dynamics, however, remain largely unknown in wild populations, mainly because of the difficulty in extensive/intensive field surveys at multiple locations. Here, I integrate results of ecological, demographic and genetic studies to elucidate detailed population structure and to identify the mechanisms of population persistence in a stream fish. Spatial structures, such as habitat size and connectivity, are particularly important in river and freshwater networks because such ecosystems are highly vulnerable to human activities. These issues are explored by examining results from a decadal research on the stream‐dwelling Dolly Varden charr in the Sorachi River basin, Japan. More than 100 local habitats (i.e. tributaries) were examined for spatial structure of populations by, such as, species presence, population census, redd counts, analysis of population synchrony and microsatellite DNA analysis. The results indicate that (i) population demography is largely independent in each tributary, (ii) some large tributaries support self‐sustaining populations, (iii) despite small population sizes in most tributaries (<30 spawning females), local extinction is rare, except in human‐influenced areas and (iv) probabilities of extinction are likely reduced by immigration of fish from neighbouring tributaries. The evidence suggests that Dolly Varden in this river system function as a source‐sink or mainland‐island metapopulation structure and that processes influencing these structures vary within the stream network. Overall, local populations may be highly persistent as long as local populations are well connected. I also discuss the vulnerability of stream fishes to habitat alterations.     

Male‐biased sex ratio of nonanadromous Oncorhynchus mykiss in a partially migratory population in California

Abstract – Differential rates of anadromy between males and females are common in partially migratory salmonid populations, but this pattern is not fully clear for Oncorhynchus mykiss (rainbow trout/steelhead) from the limited but mixed data available. In particular, there are very few data on sex ratios of juvenile and nonanadromous (resident) fish to help assess sex composition of various life stages and life‐history types. We used a recently developed Y‐chromosome genetic marker to assess sex ratio of stream‐dwelling (i.e., juvenile and nonanadromous) O. mykiss in a small coastal basin in central California, USA. We analysed 384 samples collected from three contiguous study reaches over 3 years. Sex ratio was 1:1 among juvenile‐sized O. mykiss (<150 mm) but highly male‐skewed (83%) among nonanadromous‐sized individuals (≥150 mm), and this sex ratio × size pattern did not differ among years or study reaches. Our results suggest that the rate of anadromy differs between males and females in this basin. Our study also demonstrates the application of new genetic markers to determine sex composition of immature and nonanadromous salmonids, which will help assess sex‐specific life‐history behaviour in partially migratory populations of O. mykiss and other species.     

Seasonal residency and movement patterns of two co‐occurring catadromous percichthyids within a south‐eastern Australian river

Abstract – Understanding movement patterns and habitat utilisation is critical for the management of diadromous fishes. An acoustic telemetry array was used to monitor 33 estuary perch, Macquaria colonorum and 39 Australian bass, Macquaria novemaculeata in the freshwater and estuarine reaches on the Shoalhaven River, south‐east Australia. On average, tagged M. novemaculeata were detected for a considerably shorter period than M. colonorum, and evidence suggested that fishing pressure may have impacted on their survival. Macquaria colonorum displayed significant shifts in seasonal and size‐related habitat use, with fish predominantly residing in deep (>5 m) areas within the middle (mesohaline) reaches of the estuary during the austral spring to autumn months. In winter, M. colonorum individuals made frequent downstream migrations, often to localised areas, within the lower estuary (LE). In contrast, M. novemaculeata were distributed in shallow (<2 m) habitats throughout the year, within the upper (oligohaline) estuarine reaches of the river, as well as in fresh water. Like M. colonorum, M. novemaculeata made extensive downstream and upstream movements, often coincident with reproductive behaviour, water temperature and increased freshwater inflows. It is postulated that the high site fidelity and repetitive homing displayed by both species is influenced by ontogenetic behaviour and prey availability. Furthermore, the extent of instream distribution by both species, and the lack of observed annual spawning migrations by some M. novemaculeata individuals, indicates the once considered ‘catadromous’ life cycle of these fishes may not be obligatory. A management approach is recommended to ensure that both these species are not over‐exploited within a portion of their instream range, thus maintaining their full reproductive potential.     

Potential impacts of climate change on growth and prey consumption of stream‐dwelling smallmouth bass in the central United States

Smallmouth bass (Micropterus dolomieu, SMB) is a broadly distributed, economically important species in the USA and Canada. Although previous research has suggested that projected climate warming may allow SMB to thrive beyond their current northern distribution, little research has been devoted to the population‐level effects of climate change on warm‐water fishes, including SMB. We modelled the impacts of projected climate change on growth of stream‐dwelling SMB along a north–south gradient in the central USA. Using downscaled regional projections from three global climate models, we generated scenarios for thermal habitat change for four populations (in Oklahoma, Missouri, Iowa and Minnesota) and used bioenergetics simulations to estimate prey consumption and growth under future projections. Bioenergetics simulations showed that prey consumption is expected to increase in all populations with moderate stream warming (2–3 °C). Growth potential is predicted to increase by 3–17% if not limited by food availability with stream warming by 2060 and was most pronounced for southern populations. For each 1 °C increase in stream temperature, SMB consumption would be expected to increase by about 27% and growth would increase by about 6%. Due to implications for species interactions, population performance and regulation of local fisheries, a better understanding of how SMB populations will respond to climate change is recommended for effective management and conservation.     

Allelic segregation of sex‐linked microsatellite markers in Nile tilapia (Oreochromis niloticus) and validation of inheritance in YY population

Stocking of all‐male fingerling produced by direct administration of male hormone 17‐α‐methyltestosterone is the most preferred method for present‐day aquaculture of the Nile tilapia Oreochromis niloticus. However, due to the growing concern of negative impact of steroid hormone in food fish, production of ‘genetically male’ tilapia, which depends on the concrete and thorough understanding of sex determination, has long been a scientific curiosity. The objective of the present study was to identify reliable sex‐linked markers and to evaluate the applicability of those markers in terms of monosex production approach. ‘XY’ neofemales were produced by using synthetic oestrogen and identified through selective breeding and progeny testing. Three females with progeny not deviating from 3:1 sex ratio (male:female) were designated as ‘XY’ neofemales and were used subsequently to produce putative YY progeny. Among the fifteen microsatellite markers tested, marker ARO172 was most informative in differentiating male and female genotypes. Twenty‐seven F₂ fish from three families were identified as putative YY males based on marker genotyping, and four of them were crossed to produce F₃ to validate marker association by progeny testing. The YY males produced 86%–100% male progeny indicating ARO172 a unique sex‐linked marker applicable in marker‐assisted selection.     

Incidence of spinal injuries in migratory Yellowstone cutthroat trout captured at electric and waterfall‐velocity weirs

The South Fork Snake River (Idaho, USA) supports a native Yellowstone cutthroat trout (YCT) population Oncorhynchus clarkii bouvieri (Richardson) threatened by non‐native rainbow trout O. mykiss (Walbaum). Electric weirs prevent rainbow trout passage into YCT spawning tributaries but may cause spinal injuries. YCT captured at electric weirs on Palisades and Pine Creeks and a control waterfall‐velocity weir on Burns Creek were X‐rayed in 2012 and 2013 to estimate spinal injury rates. Electrical pulse frequency was increased from 2012 to 2013 at the Palisades (from 11.5 to 20 Hz) and Pine weirs (13–20 Hz), and spinal injury rates were found to increase from 11.3 to 21.3% at Palisades and from 6.5 to 14.7% at Pine, while Burns injury rates remained constant (4.5% in 2012 and 6.0% in 2013), suggesting the electric weirs caused spinal injuries in YCT. Lower pulse frequencies may minimise YCT spinal injury but still prevent rainbow trout from accessing YCT spawning tributaries.     

Long‐term growth patterns in a pond‐dwelling population of crucian carp,Carassius carassius: environmental and density‐related factors

Abstract Scale samples from crucian carp, Carassius carassius (L.), collected over a 10‐year period from a population in an ornamental pond were used to examine patterns in growth as a function of environmental factors, including water temperatures. Back‐calculated standard lengths (SL) at age differed between year classes in most cases. Annual SL increments were related to temperature and age using a non‐linear growth model. Growth declined with increasing age, whereas annual SL increments increased with increasing water temperature. The best‐fit model was with the total number of summer days when air temperature exceeded 20 °C (using water temperature equivalents of air temperature). A growth model including water temperature, age, year class, relative condition and rainfall was a better fit than other models. Year‐class strength was positively correlated with water degree‐days, and year‐class strength negatively affected annual SL increments. The results indicate that within a strong year class of crucian carp, the growth of individual fish is reduced compared with weak year classes, suggesting that density negatively affects growth in ponds where resources are limited.     

Identification of sex‐specific markers and heterogametic XX/XY sex determination system by 2b‐RAD sequencing in redtail catfish (Mystus wyckioides)

Sex‐specific markers provide significant molecular basis for sex control breeding biotechnology to produce all‐male or all‐female fish in commercial breeding. Redtail catfish (Mystus wyckioides), one of the commercial bagrid catfishes distributed in Southeast Asian, which have a long sexual maturation period that can last 3–5 years and males have apparent growth advantage over females, but its sex determination system remains unknown. In this study, we first applied 2b‐RAD‐seq approach to identify three male‐specific 2b‐RAD‐tags and one male heterogametic SNP locus and validated by blast to the genome survey sequences and PCR amplification in both wild and breeding populations. To get longer sex‐specific region, we performed genome walking and obtained a 4,630 bp of Y‐specific sequence and 4,581 bp of X‐specific sequence from the 2b‐RAD‐tag ref189950 with 92.19% nucleotide identity between them. And 9,923 bp/3,935 bp of Y‐specific sequences and 8,491 bp/5,172 bp of X‐specific sequences were also identified with 77.49% and 57.07% nucleotide identity in ref208528 and ref210837, respectively. Subsequently, three different kinds of sex‐specific primers with different length products were designed based on the detected highly sex differentiated regions and could be used to distinguish males and females both in wild and artificially bred populations. What is more, the X‐specific fragment was discovered to produce the dosage effect association in females and in males. The data suggest that male heterogametic XX/XY sex determination system should exist in the redtail catfish. More significantly, the sex‐specific markers are of great value to protect wild resources and improve the efficiency of all‐male breeding practices for aquaculture in the redtail catfish.