Salamandra infraimmaculata Citizen science project
The Haifa Salamander Monitoring Project was initiated and led by local volunteers, collaborating with several local organizations dealing with conservation, research, and environmentalism. An initial group of volunteers with research and conservation backgrounds designed the survey protocol and routes and recruited a larger team of volunteers, trained them to track and safely capture the salamanders, and supervised the teams performing the surveys. Each team of volunteers included a team leader from the core group of volunteers who was specifically trained in safely handling the animals, performing the required measurements and determining the animals’ sex. The practical training was conducted in the field by the head of the salamander project (O. Rybak) and only upon its completion a team leader would be allowed to handle salamanders independently. The rest of the volunteers were required to go through an orientation session with the head of the project before taking part in the surveys.
The volunteers walked in teams of 3–4 along a constant route in each survey site, always at nighttime, scanned the path using flashlights, and documented every salamander they spotted along their path. They measured its length (snout to tip of tail, and occasionally the snout-to-vent length was measured additionally), weighed it, photographed its unique dorsal spot pattern for later individual identification, and documented the capture location. All of the measurements above were performed by a specific team member with the required training. The volunteers additionally documented the temperature and relative humidity during each survey. The data includes the observations from the main survey (Wadi Lotem: 2016–2022, Wadi Ahuza: 2017–2021), casual observations of salamanders in the city of Haifa during the same years, and observations of salamanders captured from the Wadi Lotem population by members of the Haifa Zoo staff during the years 2007–2009. The volunteers additionally noted possible hazards to the salamanders such as feral cats, discarded trash, signs of water contamination, or other possible threats the were spotted during the survey, as well as the presence of salamander larvae or other amphibian species in the breeding sites.
In addition to the engagement of the project participants, the project included additional efforts to inform and engage the community, including posting signs in the breeding sites, free lectures about the salamanders' biology, social media activity, and the operation of information booths around the city of Haifa. Interviews and questionnaire of the project volunteers were not conducted for this study.
The surveys and all handling of animals were conducted under the Israel Nature and Parks Authority (INPA) permits numbers 2018/42061, 2019/42368, and 2020/42648, only researchers and volunteers who were specifically listed in these permits and received the training described above handled the studied animals, and all methods were carried out in accordance with relevant guidelines and regulations. No animals were harmed in this study, and none were held in captivity. All handling in the field (photography, weighting, and measuring of salamander length) followed the guidelines required by the ethical committee of the Hebrew University of Jerusalem.
Study site
The S. infraimmaculata survey took place within the Carmel Mountain range of northern Israel, which is the southernmost edge the global distribution of S. infraimmaculata. The Carmel was originally covered by Mediterranean woodland, with numerous caverns and springs as suitable habitats, shelters, and breeding sites for salamanders of this species. The urbanization of the region which occurred gradually since the mid-20th century altered and disturbed many of these habitats, and its effects on the salamander population are not fully understood (Degani et al., 2019). The habitats in the study sites were both altered by their proximity to the city of Haifa, including wildfire, water pollution, water body alterations, discarded waste, and the presence of feral cats and dogs. Concerns regarding the state of the resident salamander populations motivated the Haifa Salamander Monitoring Project.
Data analysis
We manually recognized recaptures of individuals from the pictures taken during the surveys using their unique dorsal spot patterns.
The data from the last salamander sampling season in Wadi Ahuza (winter of 2021–2022) was not yet processed at the time of this analysis and was therefore excluded from it., In comparisons we conducted between the two population or between males and females which were not directly concerned with growth rate, we averaged multiple measurements of the same individuals when more than a single measurement of an individual was available (unless otherwise stated). The data was analyzed in the Rstudio platform(Allaire, 2012) using the packages toolsForAtlas, ggplot2 (Wickham et al., 2016), Dplyr (Mailund, 2019),tidyverse(Wickham & Wickham, 2017) ggpubr (Kassambara & Kassambara, 2020), Boot (Canty, 2002), leaflet (Cheng et al., 2019), and MASS (Ripley et al., 2013).
Growth rate and age estimation
To determine the salamanders' ages, we sought to derive a function that describes their growth throughout their lives (will be marked as L(t), noting the snout to tip-of-tail length as a function of time). In this analysis, we could not use direct regression methods since we do not have any data about any of the salamanders' ages. However, the L(t) function derived for similar species(Najbar et al., 2020) and for larvea of salamanders of this species(Warburg et al., 1979) were exponential.
Therefore, if we assume the L(t) function for the adults of this species is exponential as well, we can assert that a linear link exists between a salamander’s growth rate (\(\frac{d}{dt}{L}_{\left(t\right)}\)) and its length (L(t)), as is generally true for simple exponential functions. The differential equation representing this link is shown below::
$$\frac{d}{dt}{L}_{\left(t\right)}= a*{L}_{\left(t\right)}+b$$
Since we had multiple observations of salamanders from consecutive years, a linear regression between annual growth([length at year x + 1]- [length at year x]) and the average length during the year of growth length (([length at year x + 1] + [length at year x])/2) could be performed to derive a and b.
The solution for the differential equation is:
$${L}_{\left(t\right)}=C{e}^{at}-\frac{b}{a}$$
Where a is the growth constant (k), -\(\frac{b}{a}\) is the asymptotic length and C is the difference between the asymptotic length and the initial length. The initial length, meaning the mean length of salamanders when they complete their metamorphosis, was the only parameter which we did not derive directly from our data, and was instead taken from a previous study on this species in northern Israel(Goldberg et al., 2012). From the same set of parameters, a reverse growth function- length to age – could be derived:
$${L}_{\left(length\right)}^{-1}=\frac{\text{ln}\left(\frac{length+\frac{b}{a}}{C} \right)}{a}$$
and used to convert the salamanders' measured lengths to age estimations. However, since \({L}_{\left(t\right)}\) approaches an asymptote, from a certain point \({L}_{\left(length\right)}^{-1}\) becomes extremely sensitive to small differences in length, producing unreliable results. We determined the upper limits of the reliability of \({L}_{\left(length\right)}^{-1}\)as the point at which the yearly growth rate - \(\frac{d}{dt}{L}_{\left(t\right)}\)- is 0.5 cm/year since 0.5 cm was the measurement resolution in the survey. Using 67 cases in which the same individual was measured twice within the same month we additionally calculated the mean measurement error, which was on the same scale as the measurement resolution (± 0.66 cm, SD = 0.67).
Capture-Recapture analysis
For the Capture-Recapture analysis, we excluded all observations that did not occur during the standard-effort surveys, and all individuals that did not have a distinct enough pattern for identification upon recapture. For surveys in which air temperature, relative humidity, or survey duration was missing, the average for all other surveys was used. Since our planned model structure for the S. infraimmaculata dataset required the individual covariates (sex, length) will be listed for each sampling season for all individuals, and not all individuals were captured and measured in all seasons, the missing lengths were estimated using the growth function we derived from the data.
All datasets were analyzed using the program MARK (White & Burnham, 1999). For the S. infraimmaculata data, we constructed 28 a priori population models, with different combinations of length, sex (individual covariates), air temperature, relative humidity (environmental covariates), sampling season, and sampling occasion (time dependency) as predictor variables the probabilities for individual being captured in a specific occasion, surviving from one sampling season to the next, immigrating between sampling seasons, and emigrating between sampling seasons. The models were implemented using the "robust design – Huggins p and c" (under the assumption that captures do not alter the salamander's behavior in a way that affects future captures: p = c) model structure available in MARK.
To display individuals that were longer than the maximal length allowing age estimation (24.92 cm) on the growth curve in Fig. 2B, we used the estimated mean survival rate for fully-grown adults (0.823) to simulate the age distribution of the subpopulation of salamanders longer than 24.92 cm (under the assumption that the recruitment is constant for this subpopulation) and used this distribution to produce a rough estimation of their age, based on the rank order of their lengths.
Bufotes variabilis survey
The study sites of the B. variabilis survey were the Gazelle Valley Urban Nature Park inside the city of Jerusalem and the Ein Hemmed National park in the adjacent Judean Hills region. Gazelle Valley was a highly disturbed habitat for several years, with large amounts of waste inside and outside of the water bodies. The urban nature park on the site was established in 2015, and vast rehabilitation efforts were devoted to the aquatic habitats, including a water suspension and circulation system which added permanent ponds of differing sizes to the preexisting small ephemeral water bodies. However, it is possible that the ambient pollution present in the urban runoff water which flow into those water bodies, as well as the presence of the invasive predatory fish species Gambusia affinis, does not allow some amphibian species to breed in them, to a degree they may constitute ecological traps. Our survey sought to assess the influence of these changes on the preexisting amphibian population, by determining the population size and composition and comparing them to those of a control population. The chosen control population was the toad population of Ein Hemmed National park, located near a suburban area of the Judean Hills, in which a similar water suspension and circulation system have existed for over a decade, and in which large numbers of B. variabilis were observed in our preliminary survey. MARK output does not include exact p-values for the estimated effects of environmental and individual covariates on survival and capture probability, and instead shows 95% CI for the parameter value. Where discussing the significance of different estimated effects in this analysis, we note cases in which the 95% CI of the parameter does include 0 as p ß=0 < 0.05 since the two are equivalent. All CIs as a part of the full model outputs (S2).
Field survey
We performed a series of nighttime surveys in Gazelle Valley urban nature park and in Ein Hemmed national park in order to assess the population size and composition of B. variabilis in both sites, while documenting their breeding activity, possible hazards, and the presence of other amphibian species. We recorded all amphibian observations and their location but only members of the species Bufotes variabilis and Hyla savignyi were photographed alongside a scale bar, and their snout-to-vent lengths were measured using the scaled photographs. We included in the route the approachable shorelines of all known water bodies in both sites and recorded the presence of tadpoles and eggs, as well as breeding activity by adults of the surveyed species. We performed the surveys along a constant route, during the evening hours, and documented the air temperature, relative humidity, survey start time, and duration for each survey. No more than two people took part in each survey.
We additionally performed two daytime surveys in the water bodies of Gazelle Valley Urban Nature Park and recorded the amounts of amphibian tadpoles, eggs, and other marine organisms acquired after 10 net swipes, in three different depth categories .
For the B. variabilis data from Ein Hemmed National park, we constructed 6 a priori models with combinations of survey duration, sampling occasion, sex, and length as predictor variables of the probability of an individual being captured on a specific occasion. The models were implemented using the "Closed capture - Huggins p and c" (also assuming p = c) available in MARK. The B. variabilis data from Gazelle Valley Urban Nature Park was analyzed using the " Closed capture - full-likelihood" model structure available in MARK.