﻿A taxonomic revision of ten whitefish species from the lakes Lucerne, Sarnen, Sempach and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae)

﻿Abstract The taxonomy of the endemic whitefish of the lakes of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed and revised. Lake Lucerne harbours five species. Coregonusintermundiasp. nov. and C.suspensussp. nov., are described. Coregonusnobilis Haack, 1882, C.suidteri Fatio, 1885, and C.zugensis Nüsslin, 1882, are redescribed. Genetic studies have shown that C.suidteri and C.zugensis are composed of several distinct species endemic to different lakes. The names C.suidteri and C.zugensis are restricted to the species of lakes Sempach and Zug, respectively. The whitefish populations previously referred to as C.suidteri and C.zugensis from Lake Lucerne are described as C.litoralissp. nov. and C.muellerisp. nov., respectively. Furthermore, the whitefish from Lake Zug that were previously referred to as C.suidteri are described as C.supersumsp. nov. A holotype is designated for C.supersum that was previously one of two syntypes of C.zugensis. The other syntype is retained for C.zugensis. Coregonusobliterussp. nov. is described from Lake Zug, and C.obliterus and C.zugensis from Lake Zug are extinct. Finally, we describe C.sarnensissp. nov. from lakes Sarnen and Alpnach. Coregonussuidteri from Lake Sempach shows strong signals of introgression from deliberately translocated non-native whitefish species, which questions if the extant population still carries a genetic legacy from the original species and thus may need to be considered extinct. Coregonussuspensus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance. It is therefore compared to all known and described species of Lake Constance: C.wartmanni Bloch, 1784, C.macrophthalmus Nüsslin, 1882, C.arenicolus Kottelat,1997, and C.gutturosus Gmelin, 1818.


Introduction
The European whitefish (Coregonus spp.) are a classic example of recent postglacial adaptive radiations spanning the Palearctic temperate zone with several lakes in the boreal, subarctic, or pre-alpine regions harbouring multiple coexisting and closely related species (Steinmann 1950;Hudson et al. 2007). Many of these radiations diversified after the most recent glacial maximum approximately 15,000 years ago and comprise of evolutionary young taxa, with up to six genetically and phenotypically differentiated species occurring in single lakes of the pre-alpine region (Bernatchez 2004;Østbye et al. 2005;Hudson et al. 2007Hudson et al. , 2011Hudson et al. , 2016Kottelat and Freyhof 2007;Doenz et al. 2018;Jacobs et al. 2019;Selz et al. 2020;De-Kayne et al. 2022;Frei et al. 2022a, b). The repeated diversification of sympatric whitefish in many lakes have either arisen through a combination of sympatric and allopatric speciation in boreal and subarctic lakes (Scandinavia: Østbye et al. 2005;Praebel et al. 2013) or mainly through sympatric speciation from a hybridogenic ancestral population in pre-alpine lakes (Central Europe: Hudson et al. 2011). The repeated diversification of sympatric whitefish along a benthic to limnetic axis and a depth axis from shallow to deep in lacustrine environments exhibits often parallel patterns of divergence in phenotypic traits related to foraging and trophic ecology (i.e., gill raker number, benthic vs. limnetic feeding ecology, habitat depth partitioning during feeding), physiology (i.e., growth rate), and reproductive ecology (i.e., spawning season and spawning habitat varying along lake depth and along the benthic-pelagic axis) (Fatio 1890;Steinmann 1950;Østbye et al. 2005;Vonlanthen et al. 2009Vonlanthen et al. , 2012Harrod et al. 2010;Hudson et al. 2016;Doenz et al. 2018;Jacobs et al. 2019;Öhlund et al. 2020;Selz et al. 2020;De-Kayne et al. 2022;Frei et al. 2022a, b). Differentiation in phenotypic traits is often mirrored by strong reproductive isolation among sympatric whitefish species, confirming that ecologically differentiated whitefish occurring in sympatry are generally genetically clearly differentiated species (Douglas and Brunner 2002;Douglas et al. 2003;Hudson et al. 2011Hudson et al. , 2016Vonlanthen et al. 2012;Doenz et al. 2018;Feulner and Seehausen 2018;Jacobs et al. 2019;Selz et al. 2020;De-Kayne et al. 2022;Frei et al. 2022a, b).
Swiss lakes once harboured approximately 35 endemic species of whitefish native to 17 lakes, but due to anthropogenic eutrophication of lakes in the middle of the 20 th century one third of this diversity has been lost Hudson et al. 2013;Alexander et al. 2017b). The pre-alpine whitefish radiations originate from a hybridogenic ancestral population comprising of two divergent mitochondrial lineages Winkler et al. 2011). Furthermore, based on large genomic data sets the entire pre-alpine whitefish radiation is monophyletic when compared to the closest relatives from northern Germany and Scandinavia and most of the pre-alpine whitefish radiations form monophyletic groups by lake or lake system (Douglas et al. 2003;Hudson et al. 2011Hudson et al. , 2016Doenz et al. 2018;Jacobs et al. 2019De-Kayne et al. 2022Frei et al. 2022a, b;this study).
Part of the pre-alpine whitefish species diversity is still unresolved to date, despite the seminal revisions on European freshwater fish by  and Kottelat and Freyhof (2007). We recently evaluated the status of whitefish species of lakes Brienz and Thun, Switzerland, where we recognised seven species, of which four were new to science ). Here we revise the endemic, pre-alpine whitefish species diversity of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, redescribing three and describing seven species, respectively.
We studied the type material listed by  for the described species from lakes Lucerne, Sempach, and Zug (C. nobilis, C. suidteri, C. zugensis) and from Lake Constance (C. arenicolus, C. gutturosus, C. macrophthalmus, C. wartmanni). Furthermore, we studied contemporary specimens of all whitefish species from Lake Lucerne and from Lake Sarnen (C. nobilis, C. muelleri, C. litoralis, C. suspensus, C. intermundia, C. sarnensis). We also studied historical specimens of C. litoralis and C. muelleri from Lake Lucerne, of C. obliterus, C. zugensis, and C. supersum from Lake Zug and of all described species from Lake Constance.

Study lakes and whitefish species collection
Type material of all currently valid species (based on  systematic revision of the nomenclature of Swiss whitefish) was inspected in the collections of the Museum d'Histoire Naturelle, Genève (MHNG), Switzerland and in the Steinmann and Seehausen-Eawag collection of Eawag, Switzerland, now curated in the Naturhistorisches Museum Bern (NMBE). All contemporary specimens are part of the Seehausen-Eawag collection, which is planned to also be curated at a later stage at the NMBE. For the Steinmann collection some jars contain more than one fish and thus we provide the individual labels of each fish with 'Eawag' followed by the individual identification number, next to the NMBE number in brackets.
Contemporary samples of whitefish from the different lakes were obtained in the course of many projects of the Seehausen research group. Contemporary material used here was collected in the years 2004, 2005, 2007, 2011, and 2015 to 2017. Some of the fish were obtained from commercial fisheries catches. Fishing was done with monofilament bottom and pelagic gill nets of various mesh size ranging from 5 mm to 60 mm, and across many depth ranges in the limnetic and benthic habitats of the lakes Lucerne and Sarnen (see protocols in Alexander et al. (2015) and Hudson et al. (2016)). The fish come from three different sampling methods: targeted fishing in all lakes mentioned in this study on known spawning grounds Vonlanthen et al. 2012;this study), targeted fishing at one spawning site in Lake Lucerne along a depth cline ) and habitat-stratified fishing of the whole lake during the summer months in Lake Sarnen (Vonlanthen and Périat 2017).

Procedures of historical and contemporary specimen collection
The collection of contemporary specimens differed slightly between projects, but in general was as follows: upon capture, fish were anaesthetised and subsequently euthanised with appropriate concentrations of phenoxyethanol, clove oil or tricaine methanesulfonate (MS222) solutions. Muscle tissue and scales below the dorsal fin, as well as a part of the pectoral fin were taken for genetic and isotopic analysis and to determine the age of each fish. Each fish was photographed and then fixed in 4% formalin solution for at least 1 month and afterwards transferred through a series of ethanol of increasing concentration (30%, 50%) to the final concentration of 70% for storage. Permits for collecting fish in the lakes were issued by the cantons adjacent to the lakes. In the field the fish were identified to species level as good as possible. Sex and fresh mass were noted. Immature fish, where the sex could not be determined externally, were examined internally. For the historical specimens the sex could only be determined when the abdominal cavity had already been opened. The age was determined by counting the annual growth rings of four scales under a confocal microscope following Lehtonen and Nylund (1995).

Genetics
We used a data set of 1071 specimens genotyped at ten microsatellite loci. We combined existing data from Hudson et al. (2016) for the whitefish species of Lakes Lucerne, Neuchâtel, Zürich, Walen, and Constance, and from Selz et al. (2020) for the whitefish species from lakes Thun and Brienz with our new genetic data for the whitefish from Lakes Sarnen, Sempach, and Zug. To be able to combine the data set of Hudson et al. (2016) with our data ; this study), we extracted and genotyped 32 samples from Hudson et al. (2016) to be able to verify that genotyping was consistent across allele scoring panels, scorers, and sequencing machines. We found high genotyping agreement. Detailed information about DNA extractions, microsatellite amplification and scoring can be found in Selz et al. (2020).
To identify genetic clusters (K) of populations and obtain genetic assignment proportion for individuals in a dataset with all whitefish species from Lakes Lucerne, Sarnen, Sempach, and Zug we used an individual-based Bayesian clustering approach implemented in STRUCTURE (v. 2.3.4;Pritchard et al. 2000) with 200'000 burn-in steps and 300'000 MCM steps and 10 runs using the admixture and correlated allele frequency model for each assumed K from 1 to 10. The most likely K was determined with the Evanno method by comparing the LnP(D) values from 10 runs of different K values in Structure harvester (Earl and vonHoldt 2012). Deviations from Hardy-Weinberg equilibrium (HWE, 1000 permutations) for all loci per population, multilocus neutral genetic diversity within populations and pairwise genetic differentiation between populations (Fst, 1000 permutations) were calculated with Genodive (v. 3.03; Meirmans and van Tienderen 2004) (Suppl. material 1: table S1). A population-based neighbour-joining tree using Cavalli-Sforza chord distances (D CH ) was reconstructed using the software package PHYLIP 3.69 (Felsenstein 2005) and the best-tree with bootstrap support for each node (1000 replicates) was visualised with the package ape (5.3) in R (R 3.5.1; R core Team 2018).

Morphological and meristic characters
Twenty-five body, 19 head, four gill, and 12 meristic characters were obtained on 46 historical and 116 contemporary specimens with a digital calliper to the nearest 0.1 mm. When possible, measurements and counts were taken on the left side of the fish, unless a specific character was missing or deformed, in which case that character was obtained from the right side of the fish. The mean of two measurements was taken for each character, whereby the difference between two measurements had to be less than 5%. If deviance exceeded 5%, the distance was measured another two times. Over all morphological characters combined, the average deviance between two measurements was 1.5%. Not all measurements could be taken on all the historical specimens since some characters where damaged or absent, resulting in incomplete character lists for certain specimens. Characters for which we had missing values were excluded from the multivariate ratio analyses (see below). The number of characters used for each analysis is explicitly mentioned in the results section. A description and illustrations of each character can be found in Table 1 and Fig. 1. For all meristic characters the mode and for all morphological characters the mean together with the range for each species are reported. If the sample size was too small, a mode or mean could not be calculated and we report 'na' or write out the values. For the described species, the holotype is included in the range. Both sexes are included for the full range of each character of each species. Regarding pigmentation, we refer to the overall melanisation degree of the fins and the body. There is no detailed description of the exact structure of the pigmentation since we have only looked at traits that would be also possible for practitioners to measure in the field.

Morphological analyses
Since several species are extinct (C. obliterus, C. zugensis, C. suidteri, C. gutturosus), which has been attributed to anthropogenic-induced eutrophication of many lakes in Switzerland in the middle of the 20 th century with subsequent environmental changes that had effects on the morphological characters of whitefish species (e.g., gill rakers) Frei et al. 2022a, b), we didn't use the historical and contemporary specimens together to diagnose the species. Hence, specimens from contemporary samples are used to diagnose and distinguish among and between the whitefish species of lakes Lucerne and Sarnen. Specimens from historical samples are used to diagnose and distinguish among all historical specimens from Lake Zug, as well as between historical specimens of the species from the lakes Lucerne, Sempach, and Zug that were previously all grouped under C. zugensis or C. suidteri. Furthermore, specimens from historical samples of Lake Constance are compared to specimens from contemporary samples of C. suspensus from Lake Lucerne. We used multivariate ratio analysis methods in R to perform linear discriminant analysis (LDA) on morphological ratios (Baur and Leuenberger 2011;Baur et al. 2014). Analysis of morphological ratios are especially well suited in a taxonomic context (László et al. 2013). For a pairwise species comparison we ran linear discriminant analysis (LDA) on all or a part of the measured characters to calculate the first two LDA ratios of characters that best separate the two species in each of the pairwise species' comparisons. This was done among all contemporary specimens from lakes Lucerne and Sarnen and among all historical specimens from Lake Zug, as well as between historical specimens of the species from the lakes Lucerne and Zug that were  Table 1 for an explanation of the acronyms and a detailed description of each character). previously all grouped under C. zugensis or C. suidteri. This method also allows to estimate the extent of shape change with size (i.e., the contribution of allometry to these ratios) which is given as δ and describes how good shape discriminates in comparison to size (see Baur and Leuenberger 2011: 818, formula 14). In several pairwise species comparisons, we had more variables than individuals, which will not allow to calculate the best LDA ratios. In such cases we used a subset of informative characters to match the number of individuals. All the comparisons with a subset of characters are marked in the table and the respective characters that were used are listed (Tables 10, 11). We report only ratios that have shown to have little overlap and thus may be used to distinguish the species. Ratios marked in the table with an asterisk (*) have very little or no overlap with other species and could thus be used in the identification key and the species diagnoses.

Macrofossils from sediment cores
We collected and analysed seven sediment cores from Lake Sarnen that covered the periods (and beyond) of documented historical introductions of allochthonous whitefish from lakes Lucerne, Sempach, and Zug into Lake Sarnen (1888( -1900( : Heuscher 19001913-1920: Steinmann 1950. All seven cores were collected at the deepest location (51 m) of Lake Sarnen. The cores were cut in half and photographed. For the analysis the cores were divided into 2.5 cm intervals (~ 0.26 litres of sediment) for an average time interval of 3.6 years at a net sedimentation rate of 0.69 cm/year, which was obtained from γ-ray measurements of 210Pb and 137Cs (Müller et al. 2021). We analysed the cores from 50 cm downcore to the bottom of each core. The sediment was sieved through a 250 μm mesh and subsequently examined under a stereomicroscope. Sieve fractions were primarily screened for fish scales and bone fragments. Scales were photographed and compared to reference images from the 'Atlas of Fish Scales' Vol. 2 (Lehtonen and Nylund 1995).

Figure 2.
Map of Switzerland with the lakes studied; 1. Lake Constance, 2. Lake Sempach, 3. Lake Zug, 4. Lake Lucerne, 5. Lake Sarnen. On the right is a bathymetric map of Lake Lucerne with the German names of each basin (modified from Alexander et al. 2017a).

Data accessibility
All the data from this manuscript is available at Dryad Data Repository (https://doi. org/10.5061/dryad.8cz8w9gvx). The specimens used for taxonomic work in this study and in Selz et al. (2020) have been processed and given an accession number by the Naturhistorisches Museum Bern (NMBE). However, many of the specimens used for genetic work in this study have yet to be processed by the NMBE and are thus labelled in the accompanied dataset to this study with unique identifiers from the Seehausen-Eawag laboratory.

Genetics
We found K = 4 to be the most likely genetic cluster in the STRUCTURE analysis for the whitefish species of lakes Lucerne, Sarnen, Sempach, and Zug (Suppl. material 1: fig. S2). In agreement with previous work by Hudson et al. (2011) on a large AFLP data set we find that Lake Lucerne consists of two genetic clusters. One cluster (i.e., 'cluster 1' in Hudson et al. 2011) contains the species C. nobilis and C. muelleri and one cluster (i.e., 'cluster 2') contains the species C. litoralis, C. intermundia, C. suspensus and the whitefish population from Lake Alpnach. The two additional clusters in our analysis are a cluster (i.e., 'cluster 3') containing all whitefish from Lake Zug and Sempach and a cluster (i.e., 'cluster 4') containing the species C. sarnensis from Lake Sarnen. Few individuals from Lake Sempach that grouped in cluster 3 show high assignment likelihoods to cluster 2 of Lake Lucerne and vice versa. We have also identified a few individuals in Lake Sarnen that had moderately high individual assignment likelihoods to the Lake Lucerne cluster 2 and a few individuals in Lake Alpnach, a side-arm of Lake Lucerne that is connected to Lake Sarnen, that had high individual assignment likelihoods to the Lake Sarnen cluster 4 (Suppl. material 1: fig. S2). This can be attributed to the genetic legacy of deliberate cross-lake introductions of different whitefish species in the last two centuries (Heuscher 1900;Steinmann 1950). To compare our data to previous studies  we built a population-based neighbour-joining tree that contained all samples of Hudson et al. (2016) but additionally our new samples from lakes Sarnen, Zug and Sempach, Thun, and Brienz. We replaced the samples from Hudson et al. (2016) for the lakes Thun and Brienz with new samples and additional species described by Selz et al. (2020). Congruent with Hudson et al. (2016) the species group mostly by lake or lake-system, i.e., into lake-system specific speciesflocks (Suppl. material 1: fig. S2). The two species, C. acrinasus  from Lake Thun and C. suspensus from Lake Lucerne, for which previous work (Douglas and Brunner 2002;Douglas et al. 2003;Bittner 2009;Hudson et al. 2011Hudson et al. , 2016Doenz et al. 2018;De-Kayne et al. 2022) has suggested that the two species have genetic ancestry contributions from whitefish of Lake Constance, group with Lake Constance species. The few individuals identified in the STRUCTURE analysis from Lake Sarnen that have moderately high individual assignment likelihoods to the Lake Lucerne cluster 2, group in the neighbour-joining tree with one species from that cluster, namely C. litoralis. The few individuals from Lake Alpnach, which had high individual assignment likelihoods to the Lake Sarnen cluster 4 group in the neighbour-joining tree with C. sarnensis. The samples from lakes Sempach and Zug that grouped in cluster 3 also group in the neighbour-joining tree next to each other. Genetic differentiation (Fst) between the species ranged from 0.02 to 0.4 (Suppl. material 1: table S2).

Macrofossils from sediment cores in Lake Sarnen
The longest core of seven cores ranged back to the year 1849 and the oldest whitefish scales that were found date back to the years 1861-1857, at least 27 years prior to the deliberate introductions from 1888 to 1920 of alevins, fry, and adult whitefish from Lake Lucerne, Sempach, and Zug (Suppl. material 1: fig. S1). These findings together with the genetics analyses suggest that C. sarnensis is an endemic species of Lake Sarnen.
Description. Shape: Generally deep bodied with greatest body depth anterior of the dorsal fin. Dorsal profile from tip of snout to anterior origin of dorsal fin is strongly convex and ventral profile moderately convex from interorbital area to pelvic fin origin. Head short. Mouth short and sub-terminal. Rostral plate pronounced and a bit wider than deep resulting in a slightly rectangular shape. Tip of snout often blunt. Small eye with a thick and sickle cell-shaped eye-socket. Pectoral fin moderately tapered and moderately short. Dorsal fin long with anterior unbranched ray of the erected dorsal fin mostly 60-70 ° angle to body axis and slightly bent posteriorly at the end of the ray. Dorsal fin longest anteriorly and progressively shortening posteriorly with the outer margin of dorsal fin straight. Caudal peduncle stout and short with caudal fin moderately forked. Unbranched rays of anal fin slightly bent posteriorly. Anal fin longest anteriorly and progressively shortening posteriorly with the outer margin of anal fin mostly straight and only rarely slightly concave. Meristics: Few and short gill rakers. Colour: Pigmentation of fins and body overall strong in live specimens. Pectoral fin moderately pigmented at median to distal parts of the fin. All other fins are strongly pigmented. Silvery appearance along flanks with moderate to many pigmented small dots (aggregation of melanophores) on the scales along flank and dorsum. Distribution of dots bound to scale patterning such that dots are found at edge of the scales or at boundary point of two scales. Dorsally above lateral line the silvery appearance changes to a pale greenish or dark greenish blue colour. Seldomly, especially in older specimens, general greenish blue colour can have a pale mustard yellow ground colour (see also colour description in Fatio (1890) and Birrer and Schweizer (1938)). Dorsal part of head and snout around nostrils is strongly pigmented. Pre-operculum and operculum are silvery with one black spot on lower margin of the pre-operculum. Preserved specimens are pale in colouration with similar pigmentation as described for live specimens. Silvery, translucent, not coloured or unpigmented parts of body brown-yellowish, whereas pigmented parts conserved and coloured parts (dorsally above the lateral line) brownish.
Differential diagnosis. Based on contemporary specimens the total number of gill rakers of 24-32 (modes = 26 and 30) distinguishes C. litoralis from three of five of the other whitefish species of Lake Lucerne by having fewer gill rakers than the other species (34-40, mode = 38 in C. nobilis, 33-37, mode = 35 in C. suspensus, 33-43, mode = 36 in C. muelleri) (Table 13). Furthermore, the average standard length of three old contemporary specimens distinguishes C. litoralis from all other whitefish species of Lake Lucerne except for C. nobilis, where only specimens of 5 years of age or older were caught. The average standard length at 3 years of age of C. litoralis (range = 325-392 mm, Figure 3. Coregonus litoralis, Lake Lucerne, Switzerland. Contemporary (A-C) and historical (D, E) specimens A holotype, NMBE-1078103, 326 mm SL, male, freshly caught specimen (right side, reversed) B, C holotype, NMBE-1078103, preserved specimen D, E paratype, MHNG-717.046, 361.5 mm SL. Scale bars: 1 cm. mean = 353 mm) is larger than that of C. muelleri (160-232 mm, 194 mm), C. suspensus (266-315 mm, 289 mm) and C. intermundia (243-300 mm, 273 mm) (Suppl. material 1: table S3). The differential diagnoses against contemporary specimens of C. sarnensis from Lake Sarnen and against historical specimens of the three whitefish species from Lake Zug and C. suidteri from Lake Sempach are given under those species' account.
Distribution and notes on biology. Coregonus litoralis occurs in all basins of Lake Lucerne (Fig. 2). Based on genetic assignments it has been identified to be present in Lake Sarnen (Suppl. material 1: figs S2, S3). It is unclear if C. litoralis occurs naturally in Lake Sarnen or has been introduced (this is discussed in more detail in the Suppl. material 1: paragraph 1). Coregonus litoralis feeds predominantly on benthic prey (e.g., chironimid, pisidium) and parts of the year on zooplankton (e.g., bythotrephes, daphnia) (stomach content: Cysat 1661; Birrer and Schweizer 1938;isotopic signature: Selz 2008;Ingram et al. 2012). Feeding experiments with individuals of this species and other whitefish species from lakes Thun and Lucerne Roesch et al. 2013) suggestbased on the functional properties of the number of gill rakers -that the low-rakered C. litoralis feeds predominantly on benthic prey. Coregonus litoralis has a fast growth rate (Svarvar and Müller 1982;Müller et al. 2007) and is a large whitefish species. The size (i.e., standard length) at 3 years of age of C. litoralis is larger than that of C. suspensus and C. intermundia and considerably larger than that of C. muelleri (Suppl. material 1: table S3). We cannot compare its size to C. nobilis since only older individuals of C. nobilis have been caught . Coregonus litoralis has a short spawning season in winter. The peak spawning period varies over the years from mid-November to late December, which has been attributed to a decrease in lake water temperature below 7-8 °C (per. comm. from fisheries authorities of Lake Lucerne; Birrer and Schweizer 1938). The spawning season lasts for approximately two weeks and the spawning depth is mostly in very shallow waters (1-5 m) but can reach down to 30 m and rarely to 40 m in the main basins of Lake Lucerne excluding Lake Alpnach (Birrer and Schweizer 1938;Steinmann 1950;Hudson et al. 2016). In all the basins of Lake Lucerne except Lake Alpnach the spawning depth of C. litoralis overlaps with that of C. intermundia . Populations of C. litoralis in Lake Alpnach usually spawn earlier in the year than in the rest of Lake Lucerne, which has been suggested to be due to a more rapid cooling of the lake water in Lake Alpnach than in the rest of the basins of Lake Lucerne (Svarvar and Müller 1982;A. von Deschwanden and A. Blättler, pers. comm.). Coregonus litoralis mostly spawns though next to the entrance of Lake Alpnach in the adjacent basin 'Kreuztrichter' and less so directly in Lake Alpnach (this is discussed in more detail in the Suppl. material 1: paragraph 2). The spawning behaviour of C. litoralis has been recorded by Selz and Hofmann (2018). The video by Selz and Hofmann (2018) shows communal pairspawning behaviour whereby a female is often accompanied by up to three males. Towards the end of the video a pair spawning event can be observed in which the female and male align side by side and synchronically dart from near the bottom up towards the surface. This is the first observation of this behaviour in pre-alpine whitefish species; it had previously only been observed in the vendace (Coregonus albula) in an experimental setting (Karjalainen and Marjomäki 2017).
Etymology. The specific name in Latin means 'coming from the shore'. The name refers to the specific spawning habitat of this species, spawning in very shallow water of a few metres close to or directly at the lake shore. An adjective. Diagnosis. Coregonus intermundia is a medium-sized whitefish (standard length at 3 years of age: range = 243-300 mm, mean = 273) with moderate pigmentation of all fins and the body; greenish blue colour on the flanks above the lateral line; moderate number of pigmented small dots on the scales along the flank; short head (19.1-21.5% SL, mean = 20.3); sub-terminal mouth; thick (3.4-5.7% HL, mean = 4.4) and triangular-shaped eye socket; rather short and stout caudal peduncle (caudal peduncle depth: 7-8.3% SL, mean = 7.5; caudal peduncle length: 11.6-14.4% SL, mean = 12.9).
Description. Shape: Only slightly deep bodied with greatest body depth anterior of dorsal fin. Dorsal profile from tip of snout to anterior origin of dorsal fin and ventral profile from interorbital area to pelvic fin origin are moderately convex. Head moderately short. Mouth moderately long and mostly sub-terminal and rarely terminal. Lower jaw moderately wide. Rostral plate equally wide as deep, not strongly pronounced with tip of the snout often more pointed than blunt. Eye-socket thick and sickle cell-shaped. Pectoral fin moderately tapered and moderately short. Dorsal fin rather short with anterior unbranched ray of erected dorsal fin mostly 70-80° angle to body axis, almost straight and only very slightly bent posteriorly at end of the ray. Dorsal fin longest anteriorly and progressively shortening posteriorly with outer margin of dorsal fin mostly straight and rarely concave. Caudal peduncle stout and moderately short with caudal fin moderately forked. Unbranched rays of anal fin slightly bent posteriorly. Anal fin longest anteriorly and progressively shortening posteriorly with outer margin of anal fin mostly straight and only rarely slightly concave. Meristics: Moderately many and moderately long gill rakers. Colour: Pigmentation of fins and body overall moderately strong in live specimens. Pectoral fin slightly pigmented at distal parts of fin. Pelvic fin moderately pigmented at the median to distal parts of fin. All other fins strongly pigmented. Silvery appearance along flanks with moderate number of pigmented small dots (aggregation of melanophores) on scales along flank and dorsum. Distribution of dots bound to scale patterning such that dots are found at edge of the scales or at boundary point of two scales. Dorsally above the lateral line the silvery appearance changes to a pale greenish to dark greenish blue colour and sometimes with pale mustard yellow ground colour. Dorsal part of head and snout around nostrils moderately pigmented. Pre-operculum and operculum silvery with one black spot on lower margin of pre-operculum. Preserved specimens pale in colouration with similar pigmentation as described for live specimens. The silvery, translucent, not coloured or unpigmented parts of body become yellowish brown, whereas pigmented parts are conserved and coloured parts (dorsally above the lateral line) become brownish.
Differential diagnosis. The differential diagnosis against C. litoralis and C. sarnensis are given under those species' accounts.

Coregonus intermundia
Distribution and notes on biology. Coregonus intermundia occurs in all basins of Lake Lucerne (Fig. 2) except possibly in Lake Alpnach. It has been caught during the spawning season in all basins except for Lake Alpnach, where no nets were set by Hudson et al. (2016). There is no isotopic or stomach content data available for C. intermundia to infer the prey spectrum of this species. Coregonus intermundia is a medium-sized whitefish species and the size (i.e., standard length) at 3 years of age of C. intermundia is smaller than that of C. litoralis, considerably larger than that of C. muelleri and almost equal to that of C. suspensus (Suppl. material 1: table S3). We cannot compare its size to C. nobilis since only older individuals of the latter species have been caught . Coregonus intermundia has most likely a short spawning season in winter around the month of December. The spawning season lasts for approximately two weeks and the spawning depth is mostly in shallow waters (10-30 m, rarely 40 m; Hudson et al. 2016). The spawning depth of C. intermundia overlaps partially with that of C. litoralis, with the former spawning deeper than the latter .
Etymology. The specific name intermundia means in Latin 'spaces between the worlds'. It refers to the observation that this species is intermediate to C. litoralis and C. suspensus in its ecology and in some morphological characters. A noun in apposition.
Common name. This species was not recognised by local fisheries, fisheries authorities, researchers, or the public before the works of Lundsgaard-Hansen (2009) and Hudson et al. (2016), who named the species as Coregonus sp. 'benthic-intermediate' (In German: 'benthischer Schwebbalchen').

Diagnosis.
Coregonus suspensus is a medium-sized whitefish (standard length at 3 years of age: range = 266-315 mm, mean = 289 mm) with weak pigmentation of the pectoral fin and moderate pigmentation of all other fins and body; greenish blue colour on the flanks above the lateral line; none to a few pigmented small dots on the scales on the flanks; tip of the snout pointy; triangular eye socket; many and moderately long gill rakers (longest gill raker: 13.2-16.4% HL; total gill rakers number = 33-37).
Description. Shape: Only slightly deep bodied with greatest body depth anterior of dorsal fin. Dorsal profile from the tip of snout to anterior origin of dorsal fin and ventral profile from interorbital area to pelvic fin origin is straight and only rarely is dorsal profile from tip of snout to interorbital area slightly convex. Head moderately short. Mouth moderately long and subtly sub-terminal. Lower jaw moderately wide. Rostral plate equally wide as deep, not strongly pronounced with tip of snout often more pointed than blunt. Eye-socket moderately thick and sickle cell-shaped. Pectoral fin moderately tapered and moderately short. Dorsal fin rather short with anterior unbranched ray of erected dorsal fin mostly 60-70° angle to body axis and slightly bent posteriorly. Dorsal fin longest anteriorly and progressively shortening posteriorly with outer margin of dorsal fin mostly concave and rarely straight. Caudal peduncle moderately stout with caudal fin moderately forked. Unbranched rays of anal fin moderately bent posteriorly. Anal fin is longest anteriorly and progressively shortening posteriorly with outer margin of anal fin mostly concave and only rarely straight. Meristics: Many and long gill rakers. Colour: Pigmentation of fins and body overall moderately strong in live specimens. Pectoral fin slightly pigmented at distal parts of fin. Pelvic fin moderately pigmented at median to distal parts of fin. All other fins strongly pigmented. Silvery appearance along flanks with few pigmented small dots (aggregation of melanophores) on scales along flank and dorsum. Distribution of dots bound to scale patterning such that dots are found at edge of scales or at boundary point of two scales. Dorsally above the lateral line silvery appearance changes to a pale greenish or dark greenish blue colour. Dorsal part of head and snout around nostrils moderately pigmented. Pre-operculum and operculum are silvery with one black spot on lower margin of pre-operculum. Preserved specimens pale in colouration with similar pigmentation as described for live specimens. Silvery, translucent, not coloured or unpigmented parts of the body brown-yellowish, whereas pigmented parts conserved and coloured parts (dorsally above lateral line) brownish.
Differential diagnosis. The differential diagnoses against C. litoralis, C. intermundia, and C. sarnensis are given under those species' accounts. Coregonus suspensus shows genetic ancestry contributions from whitefish of Lake Constance, besides its Lake Lucerne ancestry (Douglas and Brunner 2002;Lundsgaard-Hansen 2009;Hudson et al. 2016;De-Kayne et al. 2022;this study). These seem to derive from historically documented introductions of fry of whitefish species from Lake Constance into Lake Lucerne (Svarvar and Müller 1982). Due to the uncertainty of the species origin of the translocated fry and the possibility that there may have been more historically undocumented introductions of other whitefish from Lake Constance we compare the characters of this species with those of all whitefish species from Lake Constance and all other whitefish species in Lake Lucerne.
Coregonus suspensus -Coregonus arenicolus Coregonus suspensus can be differentiated from C. arenicolus by having a shorter pelvic fin base (3.3-3.8% SL, mean = 3.7 vs. 3.9-4.6% SL, mean = 4.4), a shorter pelvic fin (15-16.1% SL, mean = 15.3 vs. 16.8-18.1% SL, mean = 17.3), a shorter pectoral fin base (3-3.2% SL, mean = 3.1 vs. 3.2-3.5% SL, mean = 3.4), an anteriorly shorter erected and depressed dorsal fin (erected dorsal fin: 16.9-17.8% SL, mean = 17.6 vs.  4,9,12,13). Distribution and notes on biology. Coregonus suspensus occurs in all basins of Lake Lucerne (Fig. 2) except possibly in Lake Alpnach. It has been caught during the spawning season in all basins except for Lake Alpnach, where no nets were set by Hudson et al. (2016). There is no isotopic or stomach content data available for C. suspensus to infer the prey spectrum of this species. Coregonus suspensus is a medium-sized whitefish species and the size (i.e., standard length) at 3 years of age of C. suspensus is smaller than that of C. litoralis, considerably larger than that of C. muelleri and almost equal to that of C. intermundia (Suppl. material 1: table S3). We cannot compare its size to C. nobilis since only older individuals of the latter species have been caught . Coregonus suspensus shows genetic ancestry contributions from whitefish of Lake Constance, besides its Lake Lucerne ancestry . We therefore also compared it to the four described species from Lake Constance, namely C. wartmanni Bloch, 1784, C. macrophthalmus Nüsslin, 1882, C. arenicolus , and the extinct C. gutturosus Gmelin, 1818. Early indications that C. suspensus may be of partially allochthonous origin, closely related to the radiation of Lake Constance with genetic contributions from Lake Lucerne, were seen in work by Douglas and Brunner (2002). They named a population from Lake Lucerne simply as 'Blaufelchen' (i.e., the local name for the species C. wartmanni from Lake Constance), which grouped in their study closest to Lake Constance taxa and another species of partially allochthonous origin from Lake Thun, C. acrinasus. More recent work confirmed these findings, showing that C. suspensus has a genetic affinity (based on pairwise DAPC, neighbour-joining tree and private allele analyses) with C. wartmanni from Lake Constance ; Suppl. material 1: fig. S3). Interestingly, C. suspensus may not just share a genetic affinity with C. wartmanni but also a phenotypic affinity. During the spawning season sexually mature individuals of C. suspensus were caught exclusively in the open water, which may suggest that they also spawn in the open water. This unique spawning behaviour has so far only been documented for individuals of C. wartmanni from Lake Constance (Brehm 1884;Fatio 1890;Steinmann 1950). Further research is needed to resolve if the same spawning behaviour is present in C. suspensus. It cannot be inferred solely based on the catch locality, although all ripe individuals of C. suspensus were caught with pelagic nets in the pelagic habitat ). This is not unique to this species though, as also C. litoralis and C. intermundia can be caught during the spawning season in the pelagic waters. However, in contrast to C. suspensus they seem to move from the pelagic into the benthic habitat at the time around sunset and are thus caught in the benthic habitat during spawning . Coregonus suspensus has most likely a short spawning season in winter around the month of December. The spawning season lasts for approx. two weeks. Since the 1940s whitefish fry have been stocked from Lake Constance (among other lakes, see discussion) into Lake Lucerne, specifically in Lake Alpnach (Svarvar and Müller 1982;E. Odermatt and J. Muggli, pers. comm.). Nothing is written about the time span of these introductions nor which quantity of fry from Lake Constance were introduced into Lake Lucerne. Steinmann (1950) reported individuals not corresponding to any of the known Lake Lucerne whitefish species and questioned if additional unknown species were residing in Lake Lucerne. Specifically, Steinmann (1950) mentions an increase of whitefish individuals in 1949-1950 that have been caught mostly in the basins 'Gersauerbecken', 'Urnerbecken' and Lake Alpnach (Fig. 2), which resemble in gill raker number individuals of C. nobilis, but which spawn in December in the upper water column (i.e., in German 'oberflächlich'). These individuals have been named by the commercial fishermen after the colouration of their dorsum, which was blueish, as 'Blaufelchen' and were even noted in the commercial fisheries statistics of Lake Lucerne for a certain time period (J. Muggli, pers. comm.). This is the same local name that is given to C. wartmanni from Lake Constance. This could possibly be the first mention of C. suspensus in the scientific literature. However, already in the year 1661 Cysat described three forms of large-type whitefish in Lake Lucerne, the 'Krautbalchen', the 'Schwembalchen' and the 'Steinbalchen' and a local fisherman, J. Blättler, mentioned in 1908 that he was able to distinguish between three forms of large-type whitefish in the lake (Muggli 2015). It is thus unclear, if C. suspensus derived from recent allochthonous stocking and/or if one of these three forms may partially be what we know today as C. suspensus.
Etymology. The specific name suspensus in Latin means being 'suspended' or 'levitating'. The name refers to the fact that this species has only been caught during the spawning season in the pelagic water column. An adjective.
Common names. This species was not recognised by the local fisheries, fisheries authorities, researchers, or the public before the work by Lundsgaard-Hansen (2009) and Hudson et al. (2016). Lundsgaard-Hansen (2009) Kottelat and Freyhof 2007;Müller 2007;Hudson et al. , 2013Hudson et al. , 2016Ingram et al. 2012;Vonlanthen et al. 2012;Alexander et al. 2017a. Diagnosis. Coregonus nobilis is a medium-sized whitefish with weak pigmentation of the pectoral and pelvic fin and moderate pigmentation of the anal, caudal, adipose and dorsal fin and body; pectoral and pelvic fin with yellowish undertone; pale olivebrown colouration on the flanks above the lateral line with pale greenish undertone that is most pronounced on dorsal part of the head; moderate number of pigmented small dots on the scales on the flanks; slender, elongated, and slightly torpedo-like body; caudal peduncle elongated (12.4-15.3% SL, mean = 13.9); tip of snout is fleshy and ranges from being square-like to roundish; large eye (eye diameter: 23.5-25.6% HL, mean = 25.6) with a thick (4.6-5% HL, mean = 4.7) and triangular eye socket; many and long gill rakers (longest gill raker: 15% HL; total gill raker number = 41).
Description. Shape: Slender body. Slender bodied with greatest body depth anterior of dorsal fin resulting in a slightly torpedo-like form. Dorsal and ventral profile similar and slightly arched. Dorsal and ventral profile from tip of snout to interorbital area mostly straight and then slightly convex to dorsal and pelvic fin origin respectively. Head moderately short. Mouth long and terminal or subtly sub-terminal. Lower jaw wide. Rostral plate equally wide as deep, quite pronounced with tip of snout fleshy and either roundish or blunt (square-like form). The eye is moderately large and that of historical specimens is larger than of contemporary specimens. Eye-socket thick and sickle cell-shaped. Pectoral fin moderately tapered and moderately long. Dorsal fin moderately long. Caudal peduncle narrow and elongated with caudal fin moderately forked and sometimes moderately to strongly asymmetrical. Meristics: Many and long gill rakers. Colour: Pigmentation of fins and body overall weak in live specimens. Pectoral and pelvic fin mostly transparent with yellowish ground colour, which is more pronounced in pectoral fin than pelvic fin. Pectoral fin rarely pigmented at distal part of fin and pelvic fin rarely moderately pigmented at median to distal parts of fin. Dorsal, anal, caudal and adipose fin moderately pigmented. Body weakly pigmented. Silvery appearance along flanks with moderate amount of pigmented small dots (aggregation of melanophores) on scales along flank and dorsum. Dorsally above the lateral line silvery appearance changes to a pale olive-brown and with a pale greenish ground colour that is most pronounced on dorsal part of head. Dorsal part of head and snout around nostrils moderately pigmented. Pre-operculum and operculum silvery with one black spot on lower margin of pre-operculum. Preserved specimens pale in colouration with similar pigmentation as described for live specimens. Silvery, translucent, not coloured or unpigmented parts of body become brown-yellowish, whereas pigmented parts are conserved and coloured parts (dorsally above the lateral line) become brownish.

Coregonus nobilis
Distribution and notes on biology. Coregonus nobilis occurs in all basins of Lake Lucerne (Fig. 2) except for Lake Alpnach (Nufer 1905). Since the species is endangered no commercial and recreational fisheries are permitted all year round (details on the decline of the population of C. nobilis and its putative extinction and its rediscovery is discussed in the Suppl. material 1: Paragraph 3). Hence, to understand the distribution of C. nobilis outside of the spawning season we can only consult historical catch records. These suggest that it was caught in large quantities and migrated heavily throughout the year within the basins of Lake Lucerne except for Lake Alpnach (Birrer and Schweizer 1936a;Steinmann 1950). Specifically, it was caught in water depths of 5-25 m in the pelagic habitats in the basins 'Kreuztrichter', 'Gersauerbecken', 'Urnerbecken', 'Vitznauerbecken' and 'Küssnachtersee' (Birrer and Schweizer 1936a;Fig. 2 (Birrer and Schweizer 1936a). It is a medium-sized whitefish species and has a moderate growth rate . It is the only whitefish species in Lake Lucerne that spawns in late summer in great water depths. The spawning season of C. nobilis stretches from late July to mid-September in water depths of 80 to 214 m (Birrer and Schweizer 1936a;Müller 2007;Vonlanthen et al. 2012;Hudson et al. 2016;Alexander et al. 2017a). During the spawning season it has been caught both historically and more recently in the inner basins of Lake Lucerne; 'Gersauerbecken' (Birrer and Schweizer 1936a;Hudson et al. 2016) and 'Vitznauerbecken' (Alexander et al. 2017a). Birrer and Schweizer (1936a) note that the spawning grounds can also be found in the deeper waters at gravel beds that are fed by nearby stream mouths. Diagnosis. Coregonus muelleri is a small whitefish species (standard length at 3 years of age: range = 160-232, mean = 194) with weak pigmentation of all fins and body; pale olive-brown colouration on the flanks above the lateral line; elongate slender body; large eye (eye diameter: 22.2-26% HL, mean = 24.1) with a subtle triangular eye socket; tip of snout pointy; many and long gill rakers (longest gill raker: 12.5-16.7% HL, mean = 14.5; total gill raker number: 33-43).
Description. Shape: Body elongated and slender. Greatest body depth anterior of dorsal fin. Ventral profile and dorsal profile similar and slightly arched. Dorsal and ventral profile from tip of snout to interorbital mostly straight and then slightly Figure 7. Coregonus muelleri, Lake Lucerne, Switzerland A holotype, NMBE-1078123, 180 mm SL, male, freshly caught specimen, (right side, reversed) B, C holotype, NMBE-1078123, preserved specimen D non-type, Eawag-59186, Lake Lucerne, 175 mm SL, male. Scale bars: 1 cm. convex to dorsal and pelvic fin origin respectively. Head long. Snout long and tip of snout if often pointed and seldomly fleshy resulting in a not pronounced rostral plate. Mouth long and terminal. Large eye with a subtle sickle cell-shaped (seldom roundish) eye-socket in the historical specimens and a mostly roundish (seldom sickle cell-shaped) eye-socket in the contemporary specimens. The eye of the historical specimens is larger than those of the contemporary specimens. Pectoral fin moderately long and tapered. Anterior unbranched ray of the erected dorsal fin ranges from almost vertically straight to an ~ 70-80° angle to body axis and only bent slightly posteriorly at end of the ray. Caudal peduncle narrow and elongated with caudal fin forked and sometimes moderately to strongly asymmetrical with often ventral part being longer. Unbranched rays of anal fin straight and rarely bent posteriorly at end of ray. Anal fin longest anteriorly and progressively shortening posteriorly with outer margin of the anal fin slightly concave. Meristics: Many and long gill rakers. Colour: Pigmentation of fins and body weak in live specimens. Pectoral fin transparent and pelvic and anal fin mostly transparent. Pectoral fin very rarely pigmented at distal part of the fin and anal and pelvic fin rarely moderately pigmented at median to distal parts of fin. Dorsal, caudal and adipose fin moderately pigmented. Silvery appearance along flanks. Dorsally above the lateral line silvery appearance changes to a pale olive-brown. Dorsal part of head and snout around nostrils moderately pigmented. Pre-operculum and operculum silvery with one black spot on lower margin of the pre-operculum. Preserved specimens pale in colouration with similar pigmentation as described for live specimens. In contemporary specimens silvery, translucent, not coloured or unpigmented parts of body become brown-yellowish, whereas pigmented parts are conserved and coloured parts (dorsally above the lateral line) become brownish. In historical specimens all body parts are brownish.
Differential diagnosis. The differential diagnoses against the contemporary specimens of C. litoralis, C. intermundia, C. suspensus, C. nobilis and C. sarnensis and against the historical specimens of C. litoralis from Lake Lucerne and C. zugensis from Lake Zug are given under those species' accounts.
Distribution and notes on biology. Coregonus muelleri occurs in all basins of Lake Lucerne (Fig. 2) except for Lake Alpnach (Steinmann 1950;J. Muggli, pers. comm.). Coregonus muelleri was (besides C. nobilis) historically and is today the most abundant and commercially important whitefish species in Lake Lucerne (Birrer and Schweizer 1935;Muggli 2015;Alexander et al. 2017a). Coregonus muelleri feeds -depending on the time of the year -on different pelagic prey (i.e., variety of zooplankton such as Bythotrephes, Daphnia, Bosmina, Copepoda, Leptodora and rarely Chironomidae) (Birrer and Schweizer 1935). It is a small whitefish species with the size at 3 years of age of C. muelleri being considerably smaller than that of C. litoralis, C. intermundia and C. suspensus (Suppl. material 1: table S3). We cannot compare its size to C. nobilis since only older individuals of the latter species have been caught ). It has a slow growth rate (Birrer and Schweizer 1935;Steinmann 1950). Coregonus muelleri has a long spawning season with pre-sumably two spawning peaks. The historical literature suggests that C. muelleri has a spawning peak in the early summer from July to August and a second peak in the late autumn to early winter from October to December at a spawning depth of between 60 to 200 m (Fatio 1890;Surbeck 1913;Birrer und Schweizer 1935;Steinmann 1950;Muggli 2015). However, according to the fishery warden J. Muggli it is unclear if these summer-spawning C. muelleri were once present in Lake Lucerne, at least in the last few centuries such summer-spawning C. muelleri have not been caught. The population of whitefish that we have described as C. muelleri was originally grouped under the species name C. zugensis. However, independent multilocus microsatellite (Suppl. material 1: figs S2, S3) and large genomic AFLP  data sets have shown that the whitefish species from Lake Lucerne and the whitefish populations of Lake Zug, are two independent genetic groups suggesting that C. muelleri is an endemic species of Lake Lucerne and should not be grouped under the name C. zugensis. Furthermore, C. muelleri can be distinguished based on morphological characters and ratios from historical specimens of C. zugensis, as well as from the other two species of Lake Zug, C. obliterus and C. supersum (see details under those species' account).
Etymology. The species is named after the late Dr. Rudolf Müller, a fisheries biologist and former department head and research group leader at EAWAG, Center for Ecology, Evolution and Biogeochemistry (CEEB) in Kastanienbaum, Switzerland. He dedicated a large part of his career to understanding the ecology of whitefish in Swiss lakes, and confirmed the re-discovery of C. nobilis.
Common name. Albeli. Table 6. Morphological and meristic data of Coregonus muelleri from Lake Lucerne, NMBE-1078123 holotype, contemporary specimen; paratypes of contemporary specimens N = 29 and paratype material of historical specimens N = 8. For males and both sexes the holotype is included in the range and mean of the contemporary specimens. Diagnosis. Coregonus sarnensis is a medium-sized whitefish (standard length at 3 years of age: range = 188-223, mean = 211) with weak pigmentation of the pectoral and pelvic fin and moderate pigmentation of the anal, caudal, adipose and dorsal fin and body; pale green to pale olive-brown colouration on the flanks above the lateral line; moderate number of pigmented small dots on the scales on the flanks; slender, elongated body; caudal peduncle mostly elongated (caudal peduncle depth: 7.1-8.6% SL, mean = 7.7; caudal peduncle length: 11.5-14.1% SL, mean = 12.6); tip of snout is fleshy, roundish, and often has an ~ 40-50° angle to the body axis anterior of the eye, such that the profile from the tip of the snout to the vertical projection where the anterior part of the eye crosses the dorsal profile is straight and afterwards slightly convex; large eye (eye diameter: 22.2-27.1% HL, mean = 23.9); many and long gill rakers (longest gill raker: 10.6-15.8% HL, mean = 13; total gill raker number: 33-40).

Coregonus muelleri
Description. Shape: Body elongated and slender. Greatest body depth anterior of dorsal fin resulting in a slightly torpedo-like form. Ventral profile and dorsal profile similar and slightly arched. Dorsal and ventral profile from tip of snout to interorbital mostly straight and then slightly convex to dorsal and pelvic fin origin respectively. Head moderately long. Snout often has an ~ 40-50° angle to body axis anterior of eye, such that profile from tip of snout to vertical projection where anterior part of eye crosses dorsal profile is straight and afterwards slightly convex. Tip of snout if often roundish and seldomly fleshy resulting in a not strongly pronounced rostral plate. Mouth thick (i.e., width of upper and lower jaw), long and often terminal and only rarely slightly sub-terminal. Large eye with a variable eye-socket shape ranging from sickle cell-shaped to roundish. Pectoral fin moderately long and tapered. Anterior unbranched ray of erected dorsal fin ranges from almost vertically straight to an ~ 70-80° angle to body axis and only bent slightly posteriorly at end of ray. Caudal peduncle often narrow and elongated (seldomly stout) with caudal fin forked. Unbranched rays of anal fin straight. Anal fin longest anteriorly and progressively shortening posteriorly with outer margin of anal fin slightly concave. Meristics: Many and long gill rakers. Colour: Pigmentation of fins and body moderate in live specimens. Pectoral fin transparent and pelvic and anal fin mostly transparent. Pectoral fin is only pigmented at distal part of fin and anal and pelvic fin are moderately pigmented at median to distal parts of fin. Dorsal, caudal and adipose fin moderately pigmented. Silvery appearance along flanks. Dorsally above lateral line silvery appearance changes from a pale green colouration (e.g., to an olive-green colouration. Dorsal part of head and snout around nostrils moderately pigmented. Pre-operculum and operculum silvery with one black spot on lower margin of pre-operculum. Along flank and dorsum moderately pigmented small dots (aggregation of melanophores) on scales. Preserved specimens pale in colouration with similar pigmentation as described for live specimens. Silvery, translucent, not coloured or unpigmented parts of body become brown-yellowish, whereas pigmented parts are conserved and coloured parts (dorsally above lateral line) become brownish.
Distribution and notes on biology. Coregonus sarnensis occurs in Lake Sarnen. It has further been identified by genetic assignments to be present in Lake Alpnach (Suppl. material 1: figs S2, S3), which it most likely colonised naturally over the River Sarner Aa. It has also been shown to be present south of the alps in Lake Maggiore. The 'Bondella' (local name of the population) of Lake Maggiore derives from translocations and has been shown to group in a neighbour-joining tree with C. sarnensis from Lake Sarnen . Lake Sarnen was once part of Lake Lucerne (connected through Lake Alpnach respectively) and got disconnected by amassing of sediments from the rivers Grosse Schlieren, Kleine Schlieren, and Grosse Melchaa several thousand years ago (Steinmann 1950;Pfiffner 2021). The occurrence of whitefish scales in sediment cores from Lake Sarnen that predate (scales found in the sediment layer of 1861-1857 (Suppl. material 1: fig. S1)) the earliest allochthonous whitefish introductions (1888) and independent genetic grouping of the Lake Sarnen population (AFLP data: Hudson et al. 2011; Microsattelite data: Suppl. material 1: figs S2, S3) from the lakes that seeded the allochthonous whitefish introductions (lakes Sempach, Zug, Lucerne) suggest that Lake Sarnen harbours an endemic whitefish species (this is discussed in more detail in the Suppl. material 1: paragraph 1). Information on the spawning season of C. sarnensis derive from two targeted spawning events by O.M. Selz and the fishery warden A. von Deschwanden in November of the year 2018 (pers. comm.). Thus, the spawning season of C. sarnensis is known only for November (although it may be stretching into December based on anecdotal information from recreational fishermen, which see large aggregations of putative whitefish in the deeper waters in December on their echosounders and in some cases they catch pike at these places with ripe whitefish in their stomachs in December) and it spawns at depth of 20 metres down to the lake bottom at 50 metres.
Description. Shape: Generally, deep bodied with greatest body depth anterior of dorsal fin. Dorsal profile from tip of snout to anterior origin of dorsal fin is strongly convex and ventral profile moderately convex or almost straight from interorbital area to the pelvic fin origin. Head short. Mouth short, wide and sub-terminal. Rostral plate pronounced and a bit wider than deep resulting in a slightly rectangular shape. Tip of snout often blunt. Small eye with a thick and mostly sickle cell-shaped eye-socket. Pectoral fin moderately tapered and moderately short. Dorsal fin long. Caudal peduncle stout and short with caudal fin moderately forked. Unbranched rays of anal fin slightly bent posteriorly. Anal fin longest anteriorly and progressively shortening posteriorly with outer margin of anal fin mostly straight and only rarely slightly concave.

Meristics:
Few and short gill rakers. Colour: Pigmentation of fins and body overall strong. Pectoral fin moderately pigmented at the median to distal parts of the fin. All other fins are strongly pigmented. Silvery appearance along the flanks. The preserved specimens have moderate to many pigmented small dots (aggregation of melanophores) on the scales along the flank and the dorsum. Dorsally above the lateral line the silvery appearance changes to a greenish blue colour. The dorsal part of the head and the snout around the nostrils is strongly pigmented. The pre-operculum and operculum are silvery with one black spot on the lower margin of the pre-operculum. Preserved specimens are pale in colouration with similar pigmentation as described for live specimens. Preserved fish are brownish in colouration.
Description. Shape: Body elongated and slender. Greatest body depth anterior of the dorsal fin. Ventral profile and dorsal profile similar and slightly arched. Dorsal and ventral profile from tip of snout to interorbital mostly straight and then slightly convex to dorsal and pelvic fin origin respectively. Head long. Snout long and tip of snout if slightly pointed resulting in a not strongly pronounced rostral plate. Mouth long and terminal. Large eye with a subtle sickle cell-shaped (seldom roundish) eye-socket. Pectoral fin long and tapered. Caudal peduncle moderately stout. Meristics: Many and long gill rakers. Colour: Pigmentation of fins and body weak in live specimens. Pectoral fin transparent and pelvic and anal fin mostly transparent. Pectoral fin very rarely pigmented at the distal part of the fin and the anal and pelvic fin rarely moderately pigmented at the median to distal parts of the fin. Dorsal, caudal and adipose fin moderately pigmented. Silvery appearance along the flanks. Dorsally above the lateral line the silvery appearance changes to a pale olive-brown. Pre-operculum and operculum with one black spot on the lower margin of the pre-operculum. Preserved specimens are brownish in colouration.
Differential diagnosis. The differential diagnoses against the historical specimens of C. supersum from Lake Zug are given under that species account.
Distribution and notes on biology. Coregonus zugensis occurred in Lake Zug and is extinct today (this is discussed in more detail in the Suppl. material 1: paragraph 4). Fatio (1885) mentions in a table three whitefish species for lake Zug 'Balchen', 'Albock', and 'Albeli', but later Fatio (1890) only mentions two whitefish species for Lake Zug, namely the 'Balchen' (Coregonus schinzii helveticus var. zugensis) and the 'Albeli-Albock' (Coregonus wartmanni compactus). Interestingly, Wagler (1937) noted two species to be present in Lake Zug with a remark that a third species may exist, but that its status is uncertain. Fatio (1890) does mention that fishermen have suggested that among the 'Albeli-Albock' there are individuals that are smaller and spawn later in the year, which they refer to as 'Albeli', when compared to the individuals they refer to as 'Albock' that are slightly larger and spawn earlier in the year. However, the specimens that Fatio (1890) could examine did not warrant this distinction and thus he suggested to group the 'Albeli' and 'Albock' under the name 'Albeli-Albock'. Fatio (1890) suggested that the 'Albeli-Albock' spawn in mid-September to mid-October in Lake Zug at depths of 150-180 metres. However, with the findings that Lake Zug did harbour three species of whitefish (see the notes on biology of C. supersum and the Suppl. material 1: paragraph 4 for details) and taking into account the spawning Table in Fatio (1885) and the reports by local fishermen from that time period (Fatio 1885, 1890) we Figure 10. Coregonus zugensis, Lake Zug, Switzerland A, B syntype, MHNG-715.093, 205 mm SL, sex unknown, preserved specimen C syntype, NMBE-1076275 , 188 mm SL, female, preserved specimen. Scale bars: 1 cm.
suggest that the 'Albeli', C. zugensis, spawned in comparison to C. obliterus ('Albock') later in the year from mid-October to late December in deep waters of the lake. Fatio (1885) states that the 'Albeli', C. zugensis, spawns in the deeper parts of the lake ('fond' in French) and that the 'Albock', C. obliterus, spawns in even deeper waters of the lake ('grand fond' in French). Fatio (1890) groups the 'Albeli-Albock' under Coregonus wartmanni compactus, which includes several other small and pelagic whitefish species from other lakes. This and the number and length of gill rakers of C. zugensis (many and long gill rakers) suggests, based on the functional properties of the number of gill rakers experimentally tested with specimens of other whitefish species from lakes Thun and Lucerne Roesch et al. 2013), that C. zugensis was feeding predominantly on zooplankton.
Etymology. The specific name zugensis refers to Zug, a city that gave its name to Lake Zug. An adjective.
Description. Shape: Body elongated and slender. Greatest body depth anterior of the dorsal fin. Ventral profile and dorsal profile similar and slightly arched. Dorsal and ventral profile from tip of snout to interorbital mostly straight and then slightly convex to dorsal and pelvic fin origin respectively. Head long. Snout often 40-50° angle to the body axis anterior of the eye, such that the profile from the tip of the snout to the vertical projection where the anterior part of the eye crosses the dorsal profile is straight and afterwards slightly convex. Snout moderately long and tip of snout quite deep with a strongly pronounced rostral plate. Mouth short and terminal to sub-terminal. Very large eye with a subtle sickle cell-shaped (seldom roundish) eye-socket. Pectoral fin short and tapered. Caudal peduncle moderately stout. Meristics: Few and very short gill rakers. Colour: Pigmentation of fins and body moderate in preserved specimens. All fins moderately pigmented at the median to distal parts of the fin. Operculum with one black spot on the lower margin of the pre-operculum. Preserved specimens are brownish in colouration.

Distribution and notes on biology.
Coregonus obliterus occurred in Lake Zug and is extinct today (this is discussed in more detail in the Suppl. material 1: paragraph 4). Fatio (1885) mentions three whitefish species for lake Zug, 'Balchen', 'Albock', and 'Albeli', but later Fatio (1890) only mentions two whitefish species for Lake Zug, namely the 'Balchen' Table 10. The first-and second-best ratios retrieved from the LDA ratio extractor of pair-wise comparisons of all or a subset of head and body characters of the contemporary specimens from the species of lakes Lucerne and Sarnen. For some comparisons only a subset of characters could be used (a-j); the respective characters that were included are listed at the end of the table. δ is a measure of how good shape discriminates in comparison to size (i.e., the smaller the less allometry). Ratios marked with an asterisk * have very little (not more than one specimen of one species overlaps with the other species) or no overlap and were thus eligible for use in the species key and the diagnoses.  (Coregonus schinzii helveticus var. zugensis) and the 'Albeli-Albock' (Coregonus wartmanni compactus). Interestingly, Wagler (1937) noted two species to be present in Lake Zug with a remark that a third species may exist, but that it's status is uncertain. Fatio (1890) does mention that fishermen have suggested that among the 'Albeli-Albock' there are individuals that are smaller and spawn later in the year, which they refer to as 'Albeli', when compared to the individuals they refer to as 'Albock' that are slightly larger and spawn earlier in the year. However, the specimens that Fatio (1890) could examine did not warrant this distinction and thus he suggested to group the two entities under the name 'Albeli-Albock'. Fatio (1890) suggest the the 'Albeli-Albock' spawn in mid-September to mid-October in Lake Zug at depths of 150-180 metres. In the  (1885) and the reports by local fishermen from that time period (Fatio 1885(Fatio , 1890 we suggest that this spawning period and depth should be accounted for 'Albock', C. obliterus. It seems based on the phenotype of C. obliterus including the spawning time and depth and the few and short gill rakers of this species, that this species must have occupied a similar ecological niche as is known for two whitefish species from two other lakes in Switzerland. C. gutturosus (today extinct) from Lake Constance and C. profundus from Lake Thun share many ecological and morphological characters with C. obliterus. More is known about the biology of these two species; C. gutturosus was (extinct today) and C. profundus is a profundal specialist feeding predominantly on benthic prey items and living and spawning in great water depths. Etymology. The name in Latin obliterus means 'erased from memory' or 'forgotten'. The name highlights that this species was forgotten for more than a century in the scientific literature. An adjective. Diagnosis. Coregonus suidteri is a large whitefish species with strong pigmentation of all fins and the body; greenish blue colour on the flanks above the lateral line; deep bodied (body depth: 25.4 and 29% SL); blunt snout; short head (20 and 22% SL); sub-terminal mouth; moderately large eye (eye diameter: 21.9 and 23.9% HL) with a thick (4.5 and 6.5% HL) and triangular-shaped eye socket; short and stout caudal peduncle (caudal peduncle depth: 7.8 and 8.7% SL; caudal peduncle length: 13.3 and 13.5% SL); many but rather short gill rakers (longest gill raker: 9.1% HL; total gill raker number: 35).

Species comparison
Description. Shape: Generally, deep bodied with greatest body depth anterior of dorsal fin. Dorsal profile from tip of snout to anterior origin of dorsal fin strongly Figure 12. Coregonus suidteri, Lake Sempach, Switzerland A, B syntype, MHNG-715.089, 311 mm SL, sex unknown, preserved specimen C syntype, MHNG-816.026, 312 mm SL, sex unknown, preserved specimen. Scale bars: 1 cm. convex and ventral profile moderately convex or almost straight from interorbital area to pelvic fin origin. Head short. Mouth short, wide and sub-terminal. Rostral plate pronounced. Tip of snout blunt. Large eye with a thick and sickle cell-shaped eyesocket. Pectoral fin moderately tapered and short. Dorsal fin long. Caudal peduncle stout and short. Meristics: Many but rather short gill rakers. Colour: Pigmentation of fins and body overall strong with a silvery appearance along the flanks and dorsally above the lateral line the silvery appearance changes to a greenish blue colour (based on preserved specimens and by the description by Fatio (1890)). The dorsal part of the head and the snout around the nostrils is strongly pigmented. Preserved fish are brownish in colouration.
Differential diagnosis. The differential diagnoses against the historical specimens of C. supersum from Lake Zug are given under that species account.
Distribution and notes on biology. Coregonus suidteri is found in Lake Sempach. Coregonus suidteri was previously thought to naturally occur in several lakes in Switzerland, namely lakes Lucerne, Zug, Sempach, Hallwil and Baldegg. Independent multilocus microsatellite (Suppl. material 1: figs S2, S3) and large genomic AFLP  data sets have shown that C. suidteri is composed of multiple species endemic to different lakes in Switzerland. Both population-based neighbour-joining tree's and individual-based population structure analysis suggest that contemporary samples of whitefish from Lake Zug, Sempach and Lucerne group into independent genetic clusters (Suppl. material 1: figs S2, S3; Hudson et al. 2011). The status of the extinct species C. cf. suidteri from lakes Hallwil and Baldegg is unresolved since no genetic material is present to date. The extant population of Lake Sempach whitefish on which these independent multilocus microsatellite and large genomic AFLP analyses are based on, show strong signals of genetic association with whitefish from Lake Zug and Lake Lucerne. As has been noted before for the other lakes in this study (and many more lakes in Switzerland) historical records report several incidences of introductions of whitefish from other Swiss, German and even North American lakes into Lake Sempach (Surbeck 1920;Steinmann 1950). Surbeck (1920) and Steinmann (1950) note that in the years from 1895-1902 there were several introductions of 'Balchen' (most likely C. litoralis and/ or C. intermundia) from Lake Lucerne into Lake Sempach. Steinmann (1950) further notes that other species of whitefish from many lakes were also introduced, but then only specifically mentions C. maraena and whitefish individuals from North America. Most likely many different whitefish species from Swiss lakes and beyond were introduced. This is not unique to Lake Sempach and was unfortunately common practice at that time. These deliberate introductions from other lakes took place after the population decline of whitefish in Lake Sempach, which were attributed to the lowering of the lake level in the 19 th century (Steinmann 1950). Prior to this population decline in 19 th century Lake Sempach seemed to harbour a large and productive whitefish fishery according to fisheries catch accountings (Steinmann 1950). Interestingly though, the catches of whitefish of the years 1418-1795 reported that the whitefish species in those times were rather small individuals (125 grams) compared to the larger individuals of the late 19 th century (375-750 grams) which led Steinmann (1950) to suggest that Lake Sempach may have harboured more than one species of whitefish. Fatio (1890) also notes that the size of the whitefish species in Lake Sempach were smaller and increased with the population decline towards the end of the 19 th century. Steinmann (1950) named the small type whitefish of Lake Sempach 'Kleiner Balchen des Sempachersees' and the large-type whitefish species 'Sempacherbalchen'. It is the latter species that is most likely represented by the type specimens of C. suidteri that were given to Victor Fatio in the 1880s by Otto Suidter (Steinmann 1950). Furthermore Steinmann (1950) suggests that the 'Sempacherbalchen' (i.e., C. suidteri), which he could examine in the last half of the 20 th century, should be regarded as a 'mixtum compositum', i.e., a mixed population composed of different whitefish species including the original large-type whitefish species of Lake Sempach. Indeed, Fatio (1890) already questioned if the small whitefish individuals from Lake Sempach would have had to be described as an independent species, which was displaced by larger individuals of a less common second whitefish species after the decline of the former. Given these uncertainties expressed both by Fatio (1890) and Steinmann (1950) regarding the number of species that were initially present in Lake Sempach, coupled with 1) a population decline in the 19 th century of smaller individuals of a putative small-type species resulting in fewer but larger individuals of a second largetype species, 2) deliberate introductions in the late 19 th and early 20 th century, and 3) a strong anthropogenic-induced eutrophication during the last half of the 20 th century in Lake Sempach, which may have been accompanied (as has been shown for other lakes) by population collapse, speciation reversal, and extinction Frei et al. 2022a, b), it has to be considered that the extant population of C. suidteri does not represent the original population of this species in Lake Sempach and thus should be considered extinct. Future work comparing individuals of the extant population of Lake Sempach with ancient DNA samples from sediment cores or museums samples may help to resolve if the extant population still carries a genetic legacy from the original species. We suggest that the extant population of whitefish in Lake Sempach are most likely a hybrid population with a possible genetic legacy of the original population of C. suidteri from Lake Sempach. According to Fatio (1885Fatio ( , 1890 C. suidteri spawned rather shallow in the month of November. Common names. Sempacherfelchen, Sempacherbalchen. Comparative material. All the fish detailed below were collected from Switzerland, Lake Constance. They are illustrated in Fig. 13 and listed in Tables 9, 12-14. Figure 13. Coregonus species of Lake Constance, Switzerland A Coregonus gutturosus, non-type, NMBE-1076232 (Eawag-248-1), 250 mm, sex unknown, preserved specimen B Coregonus arenicolus, holotype, 296 mm, NMBE-1076223 (Eawag-239-1), sex unknown preserved specimen C Coregonus macrophthalmus, syntype, MHNG-716.052, 215 mm, sex unknown, preserved specimen D Coregonus wartmanni, non-type, NMBE-1076206, 301 mm, female, preserved specimen. Scale bars: 1 cm.

Figure 14.
Illustrations of specimens of each species of Coregonus from Lake Lucerne and Sarnen. Illustrations of Lake Lucerne species are based on several individuals. Illustration of C. sarnensis is based on NMBE-1078159, 230 mm, male. Scale bar for C. sarnensis: 1 cm. Table 11. The first-and second-best ratios retrieved from the LDA ratio extractor of pair-wise comparisons of a subset of head and body characters of the historical specimens from the species of lakes Lucerne and Zug. For all comparisons only a subset of characters could be used (a-f); the respective characters that were included are listed at the end of the table. δ is a measure of how good shape discriminates in comparison to size (i.e., the smaller δ the less allometry). Ratios marked with an asterisk * have very little (not more than one specimen of one species overlaps with the other species) or no overlap and were thus eligible for use in the species key and the diagnoses.

Identification key to the species of Lake Lucerne
This identification key is based on contemporary specimens of the five species from Lake Lucerne. The key leads in two distinct ways to C. nobilis. The species key needs to be followed completely to be able to distinguish C. nobilis from all other whitefish species of Lake Lucerne.      Zug whitefish can be seen in the extant population of Lake Sempach suggesting that this population does not represent the original population of C. suidteri. It also has cast doubt if the occurrence of C. litoralis in lake Sarnen, which was part of Lake Lucerne before it's separation due to the amassing of sediments through several rivers, is of natural origin or due to such translocations. Scales retrieved from sediment cores prior to such translocations suggest that Lake Sarnen did harbour an endemic whitefish species, which we could show with contemporary specimens is genetically distinct and which we have described as C. sarnensis, but this does not resolve the origin of C. litoralis in Lake Sarnen. Furthermore, the many introductions of non-native whitefish into the mesotrophic Lake Alpnach, which is a side-arm of the oligotrophic Lake Lucerne, may explain why the whitefish from this part of the lake group genetically with whitefish from Lake Sempach and Lake Zug (Suppl. material 1: fig. S3). There has been allot of uncertainty in the scientific literature regarding the species status of the whitefish in Lake Alpnach due to the many introductions of allochthonous whitefish coupled with the large phenotypic variability found in this population (Birrer and Schweizer 1936b;Steinmann 1950;Svarvar and Müller 1982;Hudson et al. 2016). A future study incorporating a quantitative sampling campaign coupled with high throughput genomic sequencing may be able to resolve the species status of the whitefish population found in Lake Alpnach. The lack of such data did not allow us to examine if the population of whitefish found in Lake Alpnach is composed of several native whitefish with possible genetic signatures from non-native introductions or if it harbours a unique whitefish population. The translocations of Swiss whitefish have also led to the occurrence of whitefish from lakes Zug and Sarnen in two southern Swiss lakes, which naturally did not harbour whitefish. Hudson et al. (2011) could show that the populations of whitefish that are present in Lake Maggiore (local name of the population is 'Lavarello') and Lake Lugano group in a neighbour-joining tree with the extant population of whitefish from Lake Zug, C. supersum, and a second population of Lake Maggiore (local name of the population is 'Bondella') group with the whitefish species from Lake Sarnen, C. sarnensis. Lake Zug and Lake Sempach have experienced strong anthropogenic-induced eutrophication, which is often accompanied by population collapse, speciation reversal, and extinction of endemic whitefish species Frei et al. 2022a, b). This has most likely also been one of the main drivers of extinction of C. zugensis and C. obliterus in Lake Zug and possibly of C. suidteri in Lake Sempach.
In the case of Lake Zug nothing is known about the possibility of speciation reversal, whereby extinct species leave traces in genomes of extant species through introgressive hybridisation. Future research will be needed to understand if the extant whitefish population of Lake Zug and the extant populations of the lakes Maggiore and Lugano that we group to the species C. supersum shows signs of introgression of the extinct species of Lake Zug, C. zugensis and C. obliterus, respectively. Many of the unresolved Swiss whitefish diversity has been revised with this study coupled with the recent revision by Selz et al. (2020) on the whitefish diversity of lakes Thun and Brienz. However, future work using a taxonomic approach including recent advances in ancient DNA methods is still warranted to resolve the species status of extant and extinct populations in several Swiss lakes.