A synthetic phylogeny of freshwater crayfish: insights for conservation

Global conservation status of the jawed vertebrate Tree of Life

Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective.

Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865))

Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.

Towards evidence-based conservation of subterranean ecosystems

Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.

Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA

The Shelta Cave Crayfish (Orconectes sheltae) is a small, cave-obligate member of the genus Orconectes (family Cambaridae) endemic to a single cave system—Shelta Cave—in northwest Huntsville, Madison Co., Alabama, USA. Although never abundant, this stygobiont was regularly observed in the 1960s and early 1970s before the population and aquatic community in general at Shelta Cave collapsed likely in response to groundwater contamination and the loss of energetic inputs from a Grey Bat (Myotis grisescens) maternity colony that abandoned the cave after installation of a poorly designed cave gate. We conducted 20 visual surveys of aquatic habitats at Shelta Cave between October 2018 and July 2021. Although the aquatic community has not recovered, we did confirm the continued existence of O. sheltae, which had not been observed in 31 years, with observations of an adult female on 31 May 2019 and an adult male on 28 August 2020. We conducted the first phylogenetic analyses of O. sheltae and discovered that the species is most closely related to other geographically proximate stygobiotic crayfishes in the genus Cambarus in northern Alabama than members of the genus Orconectes. We advocate for recognition of this species as Cambarus sheltae to more accurately reflect evolutionary relationships of this single-cave endemic and offer recommendations for its management, conservation, and future research, as this species remains at high risk of extinction.

OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life

The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.[Evolution; open science; phylogenetics; Python; taxonomy.].

A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.

Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers

Background

The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula.

Methods

Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci.

Results

Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.

Evaluating Invasive Marbled Crayfish as a Potential Livestock for Sustainable Aquaculture

The marbled crayfish (Procambarus virginalis) is a recently discovered freshwater crayfish species, which reproduces by apomictic parthenogenesis, resulting in a monoclonal, and all-female population. The animals were widely distributed through the aquarium trade and have established numerous stable wild populations through anthropogenic releases. They are highly prevalent in Madagascar, where they have become a popular source of nutritional protein. As freshwater crayfish aquaculture in open systems is a thriving, but ecologically damaging global industry, alternatives are urgently needed. Although marbled crayfish are often branded by their invasive mode of reproduction, their overall invasiveness is not higher than for other cultured crayfish species. Furthermore, their resiliency and high adaptability provide a strong rationale for evaluating them for closed, and environmentally safe aquaculture approaches. Here we describe a novel population of marbled crayfish in a former German coal mining area that is characterized by acid and polluted water. Even under these adverse conditions, animals grew to sizes, and weights that are comparable to commercially farmed freshwater crayfish. Tailored feed development and laboratory testing demonstrated highly efficient feed conversion, suggesting a considerable capacity for sustainable production in closed systems. We further show that marbled crayfish meat can be readily introduced into European meals. Finally, chemical analysis of marbled crayfish exoskeletons revealed comparably high amounts of chitin, which is a valuable source for the synthesis of chitosan and bioplastics. Our results thus suggest that production of marbled crayfish in closed systems may represent a sustainable alternative for crayfish aquaculture.

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

Comparative morphology of crayfish mandibles, with insight into their evolution

Mandibles of representatives of the Holarctic crayfish families Astacidae, Cambaridae, and Cambaroididae were examined using SEM, and the results were analyzed in a phylogenetic framework. The intraspecific variability of the incisor process was found to be higher than its interspecific variability, mainly due to extensive abrasion of its ridge during intermolt periods. The plesiomorphic state of the crayfish mandibles highlights the dentate-crenate type of the incisor process and the extensive ribbed molar field with a multicuspidate caudal part, typical of the two parastacid crayfish examined for comparison. For Holarctic crayfish, the initial evolutionary type of the incisor is also the dentate-crenate one, but the molar field has a bowl-shaped caudal part and reduced cephalic part, both of which have been shown, for example, for Cambaroides. Similar mandibles are also widely present in American cambarids, which further evolved a blade-like incisor process (some Faxonius spp.) or a tricuspidate or double-bladed caudal molar field (some Procambarus spp.). The molar field in Astacidae crayfish is subdivided and rugose. The results of the present study indicate that little phylogenetic information is conveyed by the mandible shape at the species or genus level. Evolutionary changes are indicated mainly on the level of the main crayfish families. RESEARCH HIGHLIGHTS: Mandible shape can be an additional characteristic to distinguish crayfish families and selected genera. Obvious differences exist in the molar process rather than in the incisor ridge.

A journey on plate tectonics sheds light on European crayfish phylogeography

Crayfish can be used as model organisms in phylogeographic and divergence time studies if reliable calibrations are available. This study presents a comprehensive investigation into the phylogeography of the European stone crayfish (Austropotamobius torrentium) and includes samples from previously unstudied sites. Two mitochondrial markers were used to reveal evolutionary relationships among haplogroups throughout the species' distributional range and to estimate the divergence time by employing both substitution rates and geological calibration methods. Our haplotype network reconstruction and phylogenetic analyses revealed the existence of a previously unknown haplogroup distributed in Romania's Apuseni Mountains. This haplogroup is closely related to others that are endemic in the Dinarides, despite their vast geographical separation (~600 km). The separation is best explained by the well-dated tectonic displacement of the Tisza-Dacia microplate, which started in the Miocene (~16 Ma) and possibly carried part of the A. torrentium population to the current location of the Apuseni Mountains. This population may thus have been isolated from the Dinarides for a period of ca. 11 m.y. by marine and lacustrine phases of the Pannonian Basin. The inclusion of this geological event as a calibration point in divergence time analyses challenges currently accepted crayfish evolutionary time frames for the region, constraining the evolution of this area's crayfish to a much earlier date. We discuss why molecular clock calibrations previously employed to date European crayfish species divergences should therefore be reconsidered.

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are "evolutionary dead-ends." This implies that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave-dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a "dead-end" for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)

To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.

Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?

Australian spiny mountain crayfish (Euastacus, Parastacidae) and their ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes) may have co-occurred and interacted through deep time, during a period of major environmental change. Therefore, reconstructing the history of their association is of evolutionary, ecological, and conservation significance. Here, time-calibrated Bayesian phylogenies of Euastacus species and their temnocephalans (Temnohaswellia and Temnosewellia) indicate near-synchronous diversifications from the Cretaceous. Statistically significant cophylogeny correlations between associated clades suggest linked evolutionary histories. However, there is a stronger signal of codivergence and greater host specificity in Temnosewellia, which co-occurs with Euastacus across its range. Phylogeography and analyses of evolutionary distinctiveness (ED) suggest that regional differences in the impact of climate warming and drying had major effects both on crayfish and associated temnocephalans. In particular, Euastacus and Temnosewellia show strong latitudinal gradients in ED and, conversely, in geographical range size, with the most distinctive, northern lineages facing the greatest risk of extinction. Therefore, environmental change has, in some cases, strengthened ecological and evolutionary associations, leaving host-specific temnocephalans vulnerable to coextinction with endangered hosts. Consequently, the extinction of all Euastacus species currently endangered (75%) predicts coextinction of approximately 60% of the studied temnocephalans, with greatest loss of the most evolutionarily distinctive lineages.

The significance of droughts for hyporheic dwellers: evidence from freshwater crayfish

Freshwater biodiversity is globally threatened by various factors while severe weather events like long-term droughts may be substantially devastating. In order to remain in contact with the water or stay in a sufficiently humid environment at drying localities, the ability to withstand desiccation by dwelling in the hyporheic zone, particularly through vertical burrowing is crucial. We assessed the ability of three European native and five non-native crayfish as models to survive and construct vertical burrows in a humid sandy-clayey substrate under a simulated one-week drought. Three native species (Astacus astacus, A. leptodactylus, and Austropotamobius torrentium) suffered extensive mortalities. Survival of non-native species was substantially higher while all specimens of Cherax destructor and Procambarus clarkii survived. The native species and Pacifastacus leniusculus exhibited no ability to construct vertical burrows. Procambarus fallax f. virginalis and P. clarkii constructed bigger and deeper burrows than C. destructor and Orconectes limosus. In the context of predicted weather fluctuations, the ability to withstand desiccation through constructing vertical burrows into the hyporheic zone under drought conditions might play a significant role in the success of particular crayfish species, as well as a wide range of further hyporheic-dwelling aquatic organisms in general.

Phylogenetic species delimitation for crayfishes of the genus Pacifastacus

Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genus Pacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly, Pacifastacus includes both the widely invasive signal crayfish Pacifastacus leniusculus, as well as several species of conservation concern like the Shasta crayfish Pacifastacus fortis. Our analysis used 83 individuals sampled across the four extant Pacifastacus species (omitting the extinct Pacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genus Pacifastacus as monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method. Pacifastacus leniusculus included the majority of PSHs and was not monophyletic relative to the other Pacifastacus species considered. Several of these highly distinct P. leniusculus PSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities for Pacifastacus crayfishes in western North America, and may inform better understanding and management of P. leniusculus in regions where it is invasive, such as Europe and Japan.

Morphology and ultrastructure of the somatic cells in Astacus leptodactylus ovary

We defined the somatic environment in which female germinal cells develop, and performed ultrastructural analyses of various somatic cell types, with particular reference to muscle cells and follicle cells, that reside within the ovary at different stages of oogenesis. Our findings show that ovarian wall of the crayfish is composed of long muscle cells, blood cells, blood vessels and hemal sinuses. The follicle and germinal cells lie within a common compartment of ovarian follicles that is defined by a continuous basal matrix. The follicle cells form branching cords and migrate to surround the developing oocytes. A thick basal matrix separates the ovarian interstitium from ovarian follicles compartment. Transmission electron microscopy shows that inner layer of basal matrix invaginates deeply into the ovarian compartment. Our results suggest that before being surrounded by follicle cells to form follicles, oogonia and early previtellogenic oocytes reside within a niche surrounded by a basal matrix that separates them from ovarian interstitium. We found coated pits and coated vesicles in the cortical cytoplasm of previtellogenic and vitellogenic oocytes, suggesting the receptor mediated endocytosis for transfer of material from the outside of the oocytes, via follicle cells. The interstitial compartment between the inner muscular layer of the ovarian wall and the basal matrix of the ovarian follicle compartment contains muscle cells, hemal sinuses, blood vessels and blood cells. Granular hemocytes, within and outside the vessels, were the most abundant cell population in the ovarian interstitium of crayfish after spawning and in the immature ovary.

Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency

Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.