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Temperature is most cited as a factor controlling rates of growth in larval fishes and contributing to variable growth (Strydom et al. 2014a, Houde 2016). Additionally, it is clear that prey availability also exercises control over growth (Peck et al. 2012b), although the evidence is not always clear‐cut (e.g. Leggett & Deblois 1994). For estuary‐associated taxa, reported mean, weight‐specific growth rates (G) of larvae vary at least 16‐fold (G = 0.022 to 0.365 d⁻¹), with taxa from warm estuarine systems growing fastest (Houde & Zastrow 1993). In the across‐taxa synthesis, expected mean values of G for estuary‐associated taxa increased by approximately 0.01 d⁻¹ (i.e. ~1%) per 1 °C increase in temperature (T), i.e. G = −0.0236 + 0.0098T. This across‐taxa relationship was similar to that for all marine fish larvae (Houde & Zastrow 1993).

Growth rates of individual taxa also vary widely and are responsive to temperature. For example, weight‐specific growth rates of the moronid Morone saxatilis larval cohorts in Chesapeake Bay varied from 0.15 to 0.35 d⁻¹ (equates to 0.19 to 0.39 mm d⁻¹) and were directly responsive to temperatures ranging from 14–24 °C (Rutherford & Houde 1995). The consequences of variability in growth rates are indicated in stage durations of M. saxatilis larvae. At 14 °C, larval M. saxatilis require 58 days to grow from 4 to 15 mm TL, but only 28 days at 24 °C. In the sillaginid Sillaginodes punctatus, early larval growth in offshore environments is positively related to temperature, as is subsequent level of recruitment in Port Phillip Bay, Australia (Jenkins & King 2006). Although a key variable for most taxa, temperature may have relatively small effects on larval growth rates of some species, for example in the pleuronectid Pseudopleuronectes americanus, in which other site‐specific factors determined variability in rates of growth in New Jersey (USA) estuaries (Sogard et al. 2001). In another example, post‐settlement Pleuronectes platessa juveniles in European estuarine and coastal nurseries exhibited inter‐annual variability in growth that depended on temperature, but within‐year variability in growth rates was nursery‐specific and apparently highly dependent on factors other than temperature (Ciotti et al. 2014). Given higher mortality rates and selective predation on small or slow‐growing young fish (Sogard 1997), variability in growth and stage duration during early life potentially can control levels of recruitment.

Mortality rates of early‐life stages often exceed 10% d⁻¹ and larval‐stage cumulative mortality often exceeds 99% (Houde 2002). Predation usually is presumed to be the major direct cause of mortality to fish eggs and larvae (Bailey & Houde 1989), but environmental factors at lethal or stressful levels also contribute to mortality and are discussed in examples and case studies presented below. The highest mortality rates of estuary‐dependent species, as for most marine species, generally occur in the egg and early‐larval stages. These high and variable rates may act to coarsely set levels of recruitment in estuary‐dependent fishes, as in the pleuronectid Pleuronectes platessa (Van der Veer 1986, Nash & Geffen 2012). Size‐ or growth‐rate selective mortality, usually from predation, not only can obscure starvation as the source of mortality (by selective removal of small or slow‐growing individuals) but it also contributes to shifts in size distributions, age structure and apparent growth rates of survivors, complicating interpretation of dynamics in early life (Houde 2002, Houde & Bartsch 2009).

For serial‐spawning, estuarine species and those spawning over a protracted season, mortality rates of daily or weekly cohorts of early‐life stages may be highly variable as in the moronid Morone saxatilis in Chesapeake Bay (Houde 1996), the rates reflecting the changing environmental conditions in the estuary. Factors exercising control over survival are principally trophodynamic (e.g. attributable to prey availability and predation) and hydrodynamic (e.g. estuarine circulation and hydrography). In general, mortality rates of early‐life stages appear to be more variable than growth rates (Houde 1997b), indicating that mortality is a stronger driver of recruitment variability than is growth.

Temperature is often linked to, or correlated with, survival of young stages of estuary‐dependent fishes. At temperatures above or below the range of physiological tolerance, mortality may be directly attributable to lethal temperature, or linked to other co‐occurring stresses such as summer hypoxia. Event‐related mortalities of young fish may be common in small and shallow estuarine ecosystems that are poorly insulated against temperature variability generated by local or regional weather events (e.g. Dey 1981, Rutherford & Houde 1995). Under many circumstances, temperature‐related mortality may occur primarily as an indirect response to stresses that control physiological rates, prey consumption, swimming activity, encounters with predators or possibly diseases. These indirect effects influence mortality through controls on growth rate and stage duration, or by altering behaviours (e.g. swimming speeds and behaviours that affect prey encounter or predator avoidance) (Houde 2002, Houde & Bartsch 2009).

Mortality of estuarine fish larvae may be less tightly coupled to temperature than is growth, although temperature clearly is important. At the ecosystem and community (across‐taxa) levels, expected mortality of estuarine fish larvae increases with increasing temperature (Houde & Zastrow 1993), indicating that young, estuary‐dependent fishes from warm, low‐latitude ecosystems usually experience higher daily mortality rates than larvae of species from temperate and high latitudes. In a synthetic analysis, daily instantaneous mortality rates (M) of larval‐stage, estuary‐dependent fishes ranged from 0.05 to 0.52 d⁻¹ (4.9 to 40.5% d⁻¹) and expected mortality increased by approximately 0.01 d⁻¹ for each 1 °C increase in temperature (M = 0.0277 + 0.0137T), a rate similar to that for weight‐specific growth rate (G) of estuarine fish larvae. In the Houde & Zastrow (1993) synthesis, rates of M and G of individual species of estuary‐dependent larval fishes were positively correlated, indicating a strong, although coarse, concordance between the rate of instantaneous mortality (M) and G that depends on an ecosystem's temperature.

When recruitment outcomes of marine and estuarine fishes are evaluated with respect to stage‐specific survival, the levels and variability of mortality rates during the early‐larval stage were, in many cases, found to be the most important determinant of recruitment level (e.g. Bannister et al. 1974, Secor & Houde 1995, Martino & Houde 2012, Van der Veer et al. 2015). Mortality rates of juvenile estuarine fishes are lower than that for eggs and larvae (Bergman et al. 1988, Scharf 2000, Martino & Houde 2012, Nash & Geffen 2012). A long juvenile stage (weeks to years, depending on species) can, however, generate high and variable cumulative mortality that may determine, and can adjust or stabilise, recruitment levels (Beverton & Iles 1992, Kimmerer et al. 2000, Houde 2008). In temperate and high‐latitude estuaries, overwinter mortality of pre‐recruit juveniles is particularly important as a process that regulates recruitment, in which age‐0+ juveniles in poor nutritional condition experience high and size‐selective mortality (Hurst & Conover 1998, Hare & Able 2007, Hurst 2007).

Mortality of marine organisms generally declines with size in a predictable, if variable, way (e.g. Peterson & Wroblewski 1984) where M = aW ^b with the exponent b relating decline in mortality (M) relative to mass (W) theoretically equal to −0.25. In an analysis on larvae that included three estuary‐dependent taxa (Houde 1997b), Anchoa mitchilli, Alosa sapidissima and Morone saxatilis, mortality rates did decline with respect to mass. But, rates of decline were faster than predicted (exponents −0.32 for A. mitchilli; −0.39 for A. sapidissima and −0.42 for M. saxatilis), indicating that the probability of dying declines rapidly with respect to ontogeny and growth. The exponent b in the relationship of M to W for larvae of these three species also varied inter‐annually. The ratio of instantaneous mortality rate (M) to weight‐specific growth rate (G) is the physiological mortality rate (Beyer 1989). The trend in this ratio for the three species in the example, with respect to ages or sizes at which M/G became <1 (i.e. the ‘critical size’, an indicator that a cohort or year class was gaining biomass) varied amongst the species (Houde 1997b). The levels of M/G, and its trend in the earliest days posthatch, identify cohorts that have the potential to contribute strongly to recruitment (Cowan et al. 2000).

Estimating mortality rates of early‐life stages is difficult, especially so in large, open marine systems (Houde 2002) where the earliest life stages of many estuary‐dependent and ‐associated fishes are found. Within estuaries, estimating mortality is more tractable, particularly so in small systems that can be quickly and repeatedly sampled, or for which estuarine retention times are known. Dispersion losses in the estuary may be less problematic in biasing abundance estimates of eggs and larvae than in continental shelf and open ocean systems. Dispersion losses may constitute a large fraction of mortality when eggs or larvae are advected away from nursery areas and may confound estimates of mortality (Helbig & Pepin 1998).

In well‐designed studies, some estuaries can be rapidly sampled for eggs and larvae within time periods much less than estuary residence times, facilitating estimation of egg and larval abundances. In estuaries, experimental approaches also are possible to evaluate growth and estimate mortality of larvae and small juveniles. For example, releases of hatchery‐produced, chemically marked larvae can be effective to conduct mark‐recapture research on early‐life stages in estuarine systems (Tsukamoto 1985, Tsukamoto et al. 1989, Secor et al. 1995, 2017).