Whole Snake Genomes from Eighteen Families of Snakes (Serpentes: Caenophidia) and Their Applications to Systematics.

We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of UCEs and AHEs, as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other, and strongly congruent with previously published snake phylogenies. To show additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (Stegonotus admiraltiensis and Tropidonophis doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus cucullatus and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.

Neotropical Turtle Blood Flukes: Two New Genera and Species from the Amazon River Basin with a Key to Genera and Comments on a Marine-Derived Parasite Lineage in South America.

Two new genera and species of freshwater turtle blood flukes (TBFs) are described herein based on specimens infecting the nephritic and mesenteric blood vessels of "matamatas" (a side-necked turtle, Chelus fimbriata [Schneider, 1783] [Pleurodira: Chelidae]) from the Amazon River Basin, Peru. These taxa comprise the first-named species and the first-proposed genera of freshwater TBFs from the continent of South America. A new comparison of all TBF genera produced 6 morphologically diagnosed groups that are discussed in light of previous TBF classification schemes and a novel phylogenetic hypothesis based on the nuclear large subunit ribosomal DNA (28S). Considering external and internal anatomical features, species of the new genera (Atamatam Bullard and Roberts n. gen., Paratamatam Bullard and Roberts n. gen.) are most similar to each other and are together most similar to those of several marine TBF genera. The 28S phylogenetic analysis supported the monophyly of all 6 morphologically diagnosed groups of genera. Most notably, the freshwater TBFs of South America comprise a derived group nested within the clade that includes the paraphyletic marine TBFs. Not surprisingly in light of morphology, another marine TBF lineage (Neospirorchis Price, 1934) clustered with the freshwater TBFs of Baracktrema Roberts, Platt, and Bullard, 2016 and Unicaecum Stunkard, 1925. Our results, including an ancestral state reconstruction, indicated that (1) freshwater TBFs have colonized marine turtles twice independently and that (2) the South American freshwater TBFs comprise a marine-derived lineage. This is the first evidence that TBFs have twice independently transitioned from a marine to freshwater definitive host. Marine incursion is considered as a possible mechanism affecting the natural history of marine-derived freshwater TBFs in South America. A dichotomous key to accepted TBF genera is provided.

Spirorchis spp. (Digenea: Schistosomatoidea) infecting map turtles (Cryptodira: Emydidae: Graptemys spp.) in southeastern North America: A new species, molecular phylogenies, and key to species.

Black-knobbed map turtles (Graptemys nigrinoda Cagle) and Alabama map turtles (Graptemys pulchra Baur) were infected with several blood flukes in Alabama (southeastern North America). Spirorchis paraminutus Roberts & Bullard n. sp. differs from its congeners by having a body that is 12-24× longer than wide, a testicular column of 10 testes that is 1/5-1/4 of the body length and located far posterior to the caecal bifurcation (the anterior-most testis is located in the posterior body half), and a common genital pore that is ventral to the ovary and 1/4-1/3 of the body length from the posterior extremity. These turtles and an Escambia map turtle (Graptemys ernsti Lovich & McCoy) were infected with Spirorchis elegans Stunkard, 1923, Spirorchis scripta Stunkard, 1923 and two innominate species of Spirorchis MacCallum, 1918. Phylogenetic analyses of the internal transcribed spacer region (ITS2) and large subunit rDNA (28S) recovered a monophyletic Spirorchis and the new species sister to Spirorchis collinsi Roberts & Bullard, 2016.

A new genus and species of turtle blood fluke (Digenea: Schistosomatoidea) from the Mekong snail-eating turtle, Malayemys subtrijuga (Schlegel & Müller) (Testudines: Geoemydidae) in Vietnam, with a reassessment of related Asiatic turtle blood flukes and molecular phylogeny.

Platt sinuosus Roberts & Bullard n. g., n. sp. (type-species) infects the kidney and mesenteric blood vessels of Mekong snail-eating turtles, Malayemys subtrijuga (Schlegel & Müller), in the Mekong River Basin. Species of Platt Roberts & Bullard n. g. are unique by the combination of having a papillate ventral sucker, vasa efferentia that are dorsal to the gonads, a massive cirrus-sac that is directed anteriad or laterad, and a vitellarium that surrounds the intestinal caeca. The new species resembles Platt ocadiae (Takeuti, 1942) Roberts & Bullard n. comb. but differs from it by having an external seminal vesicle that overlaps with or is immediately posterior to the level of the ventral sucker. Seven species previously of Hapalorhynchus Stunkard, 1922 are reassigned herein to Platt: P. odhnerensis (Mehra, 1933) Roberts & Bullard n. comb.; P. yoshidai (Ozaki, 1939) Roberts & Bullard n. comb.; P. ocadiae; P. oschmarini (Belous, 1963) Roberts & Bullard n. comb.; P. sutlejensis (Mehrotra, 1973) Roberts & Bullard n. comb.; P. synderi (Platt & Sharma, 2012) Roberts & Bullard n. comb.; and P. tkachi (Platt & Sharma, 2012) Roberts & Bullard n. comb. A dichotomous key to Platt spp. is provided. Hapalorhynchus sheilae (Mehrotra, 1973) Bourgat, 1990 and Hapalorhynchus mica (Oshmarin, 1971) Bourgat, 1990 are considered as species inquirendae, and Hapalorhynchus indicus (Thapar, 1933) Price, 1934 and Hapalorhynchus macrotesticularis (Rohde, Lee, & Lim, 1968) Brooks & Sullivan, 1981 are considered as species incertae sedis. Phylogenetic analysis of the large subunit rDNA (28S) showed P. sinuosus and P. snyderi to be sister taxa distinct from a monophyletic Hapalorhynchus and Coeuritrema platti Roberts & Bullard, 2016.

Morphological and molecular confirmation of Myxobolus cerebralis myxospores infecting wild­caught and cultured trout in North Carolina (SE USA).

We used microscopy and molecular biology to provide the first documentation of infections of Myxobolus cerebralis (Myxozoa: Myxobolidae), the etiological agent of whirling disease, in trout (Salmonidae) from North Carolina (USA) river basins. A total of 1085 rainbow trout Oncorhynchus mykiss, 696 brown trout Salmo trutta, and 319 brook trout Salvelinus fontinalis from 43 localities across 9 river basins were screened. Myxospores were observed microscopically in pepsin-trypsin digested heads of rainbow and brown trout from the Watauga River Basin. Those infections were confirmed using the prescribed nested polymerase chain reaction (PCR; 18S rDNA), which also detected infections in rainbow, brown, and brook trout from the French Broad River Basin and the Yadkin Pee-Dee River Basin. Myxospores were 9.0-10.0 µm (mean ± SD = 9.6 ± 0.4; N = 119) long, 8.0-10.0 µm (8.8 ± 0.6; 104) wide, and 6.0-7.5 µm (6.9 ± 0.5; 15) thick and had polar capsules 4.0-6.0 µm (5.0 ± 0.5; 104) long, 2.5-3.5 µm (3.1 ± 0.3; 104) wide, and with 5 or 6 polar filament coils. Myxospores from these hosts and rivers were morphologically indistinguishable and molecularly identical, indicating conspecificity, and the resulting 18S rDNA and ITS-1 sequences derived from these myxospores were 99.5-100% and 99.3-99.8% similar, respectively, to published GenBank sequences ascribed to M. cerebralis. This report comprises the first taxonomic circumscription and molecular confirmation of M. cerebralis in the southeastern USA south of Virginia.

Emendation and new species of Hapalorhynchus Stunkard, 1922 (Digenea: Schistosomatoidea) from musk turtles (Kinosternidae: Sternotherus) in Alabama and Florida rivers.

Hapalorhynchus Stunkard, 1922 is emended based on morphological study of existing museum specimens (type and voucher specimens) and newly-collected specimens infecting musk turtles (Testudines: Kinosternidae: Sternotherus spp.) from rivers in Alabama and Florida (USA). Hapalorhynchus conecuhensis n. sp. is described from an innominate musk turtle, Sternotherus cf. minor, (type host) from Blue Spring (31°5'27.64″N, 86°30'53.21″W; Pensacola Bay Basin, Alabama) and the loggerhead musk turtle, Sternotherus minor (Agassiz, 1857) from the Wacissa River (30°20'24.73″N, 83°59'27.56″W; Apalachee Bay Basin, Florida). It differs from congeners by lacking a body constriction at level of the ventral sucker, paired anterior caeca, and a transverse ovary as well as by having a small ventral sucker, proportionally short posterior caeca, nearly equally-sized anterior and posterior testes, a small cirrus sac, and a uterus extending dorsal to the ovary and the anterior testis. Specimens of Hapalorhynchus reelfooti Byrd, 1939 infected loggerhead musk turtles, stripe-necked musk turtles (Sternotherus peltifer Smith and Glass, 1947), Eastern musk turtles (Sternotherus odoratus [Latreille in Sonnini and Latreille, 1801]), and S. cf. minor. Those of Hapalorhynchus cf. stunkardi infected S. minor and S. odoratus. Sternothorus minor, S. peltifer, and S. cf. minor plus S. minor and S. odoratus are new host records for H. reelfooti and H. cf. stunkardi, respectively. This is the first report of an infected musk turtle from the Coosa and Tallapoosa Rivers (Mobile-Tensaw River Basin), Pensacola Bay Basin, or Apalachee Bay Basin. Sequence analysis of the large subunit rDNA (28S) showed a strongly-supported clade for Hapalorhynchus.

Acipensericola glacialis n. sp. (Digenea: Aporocotylidae) from heart of lake sturgeon Acipenser fulvescens Rafinesque (Acipenseriformes: Acipenseridae) in the Great Lakes Basin, Lake Winnebago System, USA.

Acipensericola glacialis n. sp. infects the heart of lake sturgeon, Acipenser fulvescens (Rafinesque), in the Lake Winnebago System and differs from its only congener, Acipensericola petersoni Bullard, Snyder, Jensen & Overstreet, 2008, by having a dendritic intestine, deeply-lobed testes, a post-ovarian oötype, and a common genital pore that is medial to the dextral caecum. Acipensericola petersoni has a non-dendritic intestine, testes that are not deeply lobed, an oötype that is at level of the ovary (ventral to the ovary), and a common genital pore that is dorsal to the dextral caecum. Comparison of the large (28S) and small (18S) sub-unit ribosomal DNA and internal transcribed spacer 2 (ITS2) regions between specimens of A. glacialis n. sp. and A. petersoni revealed 13 (of 1,621 nt; 99.2% similarity in the 28S), 8 (of 1,841 nt; 99.9% similarity in the 18S), and 11 (of 442 nt; 97.5% similarity in the ITS2) nucleotide differences. Collectively, these results comprise an unexpectedly high degree of morphological and molecular similarity given the geographical (Mississippi River Basin vs Great Lakes Basin) and phylogenetic (Polyodontidae vs Acipenseridae) separation of these hosts but seemingly did not reject a previous hypothesis concerning lake sturgeon dispersal from the Mississippi Refugium following the Wisconsin glaciation ~18,000 years ago. The new species is the first nominal blood fluke described from a sturgeon.

Revision and New Species of Vasotrema Stunkard, 1926 (Digenea: Schistosomatoidea): Turtle Blood Flukes of North American Softshell Turtles (Testudines: Trionychidae: Apalone spp.).

Gulf Coast spiny softshell turtles, Apalone spinifera aspera (Agassiz, 1857) (Testudines: Trionychidae) from Canoe Lake (33°47'56.16″N, 86°29'25.02″W; Springville, Alabama) and Round Lake (32°41'50.91″N, 87°14'30.39″W; Perry Lakes State Park, Marion, Alabama), were infected by V. robustum Stunkard, 1928 , Vasotrema longitestis Byrd, 1939 , and Vasotrema rileyae n. sp. The new species differs from its congeners by having papillate suckers, a short testis, an ovary dextral to the oviduct, and a pre-ovarian genital pore that is lateral to the ventral sucker. We studied the newly collected specimens and museum specimens of all congeners to revise the diagnosis of Vasotrema Stunkard, 1926 and redescribe and provide an updated dichotomous key to all species of the genus.

Exotic "Gill Lice" Species (Copepoda: Lernaeopodidae: Salmincola SPP.) Infect Rainbow Trout (Oncorhynchus mykiss) and Brook Trout (Salvelinus fontinalis) in the Southeastern United States.

Salmincola californiensis infected 25 of 31 (prevalence 0.8; intensity 2-35 [mean 6.6 ± standard deviation 7.7; n = 25]) rainbow trout, Oncorhynchus mykiss, from a private trout farm connected to the Watauga River, North Carolina. Salmincola edwardsii infected all of 9 (1.0; 2-43 [9.3 ± 13.0; 9]) brook trout, Salvelinus fontinalis, from Big Norton Prong, a tributary of the Little Tennessee River, North Carolina. Both lernaeopodids are well-known salmonid pathogens, but neither is native to, nor has been previously taxonomically confirmed from, the southeastern United States. Herein, we (1) use light and scanning electron microscopy to identify and provide supplemental morphological observations of these lernaeopodids, (2) furnish complementary molecular sequence data from the 28S rDNA (28S), and (3) document the pathological effects of gill infections. We identified and differentiated these lernaeopodids by the second antenna (exopod tip with large [S. californiensis] vs. slender [S. edwardsii] spines; endopod terminal segment with subequal ventral processes shorter than [S. californiensis] vs. longer than or equal to [S. edwardsii] dorsal hook), maxilliped palp (length typically ≤1/3 [S. californiensis] vs. 1/3-1/2 [S. edwardsii] subchela length exclusive of claw), and bulla (sub-circular and concave on manubrium's side [S. californiensis] vs. non-stellate [S. edwardsii]). Analysis of the 28S rDNA sequences confirmed our taxonomic assignments as demonstrated by 100% sequence similarity among the sympatric, morphologically-conspecific isolates. Histopathology revealed focal gill epithelial hyperplasia, obstruction of interlamellar water channels, lamellar fusion, and crypting of gill filaments. High intensity infections by either lernaeopodid are surveillance-worthy because they are potentially pathogenic to trout in the southeastern United States.

Prevalence of avian haemosporidian parasites is positively related to the abundance of host species at multiple sites within a region.

Parasite prevalence is thought to be positively related to host population density owing to enhanced contagion. However, the relationship between prevalence and local abundance of multiple host species is underexplored. We surveyed birds and their haemosporidian parasites (genera Plasmodium and Haemoproteus) at multiple sites across eastern North America to test whether the prevalence of these parasites in a host species at a particular site is related to that host's local abundance. Prevalence was positively related to host abundance within most sites, although the effect was stronger and more consistent for Plasmodium than for Haemoproteus. In contrast, prevalence was not related to variation in the abundance of most individual host species among sites across the region. These results suggest that parasite prevalence partly reflects the relative abundances of host species in local assemblages. However, three nonnative host species had low prevalence despite being relatively abundant at one site, as predicted by the enemy release hypothesis.

A new species of Spirorchis MacCallum, 1918 (Digenea: Schistosomatoidea) and Spirorchis cf. scripta from chicken turtle, Deirochelys reticularia (Emydidae), with an emendation and molecular phylogeny of Spirorchis.

Chicken turtles, Deirochelys reticularia (Latreille in Sonnini et Latreille) (Testudines: Emydidae) from Alabama, USA were infected by Spirorchis collinsi Roberts et Bullard sp. n. and Spirorchis cf. scripta. The new species is most easily differentiated from its congeners by the combination of having caeca that extend far beyond the genitalia, intercaecal genitalia positioned in the middle portion of the body, a testicular column that nearly abuts the caecal bifurcation, a cirrus sac positioned between the testes and ovary, a massive Mehlis' gland, an elongate, longitudinal metraterm that extends anteriad beyond the level of the ovary, a pre-ovarian genital pore, and a prominent, intercaecal Manter's organ. The specimens of S. cf. scripta differed from the holotype and published descriptions of Spirorchis scripta Stunkard, 1923 by several subtle morphological features, perhaps comprising intraspecific variation, but collectively warranted a detailed description herein. Based on examinations of the aforementioned specimens plus the holotype, paratypes and vouchers of morphologically-similar congeners, Spirorchis MacCallum, 1918 is emended to include the presence of oral sucker spines, a pharynx, lateral oesophageal diverticula ('plicate organ') and a median oesophageal diverticulum ('oeseophageal pouch'). Phylogenetic analysis of the nuclear large subunit rDNA (28S) recovered S. collinsi sister to Spirorchis picta Stunkard, 1923, > 99% similarity between S. cf. scripta and S. scripta, and a monophyletic Spirorchis MacCallum, 1918. No blood fluke infection has been reported previously from these drainages, Alabama, or this turtle species. This is the first new species of Spirorchis to be described from North America in 26 years.

Blood flukes of Asiatic softshell turtles: revision of Coeuritrema Mehra, 1933 (Digenea: Schistosomatoidea) and a new species infecting Chinese softshell turtles, Pelodiscus sinensis (Trionychidae), from Vietnam.

Coeuritrema Mehra, 1933, previously regarded as a junior subjective synonym of Hapalorhynchus Stunkard, 1922, herein is revised to include Coeuritrema lyssimus Mehra, 1933 (type species), Coeuritrema rugatus (Brooks et Sullivan, 1981) comb. n., and Coeuritrema platti Roberts et Bullard sp. n. These genera are morphologically similar by having a ventral sucker, non-fused caeca, two testes, a pre-testicular cirrus sac, an intertesticular ovary, and a common genital pore that opens dorsally and in the sinistral half of the body. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) suggested that Coeuritrema and Hapalorhynchus share a recent common ancestor. Coeuritrema is morphologically most easily differentiated from Hapalorhynchus by having ventrolateral tegumental papillae and a definitive metraterm that is approximately 3-7× longer than the uterus. Coeuritrema comprises species that reportedly infect Asiatic softshell turtles (Testudines: Trionychidae) only, whereas Hapalorhynchus (as currently defined) comprises blood flukes that reportedly infect those hosts plus North American musk turtles (Sternotherus Bell in Gray) and mud turtles (Kinosternon Spix), both Kinosternidae, North American snapping turtles (Chelydridae), Asiatic hard-shelled turtles (Geoemydidae) and African pleurodirans (Pelomedusidae). Coeuritrema platti sp. n. infects the blood of Chinese softshell turtles, Pelodiscus sinensis (Wiegmann), cultured in the Da Rang River Basin (Phu Yen Province, Vietnam). It differs from C. lyssimus by having a narrow hindbody (< 1.6× forebody width), ventrolateral tegumental papillae restricted to the hindbody, a short cirrus sac (< 10% of corresponding body length), a transverse ovary buttressing the caeca, a short, wholly pre-ovarian metraterm (~ 10% of corresponding body length), and a submarginal genital pore. It differs from C. rugatus by having small ventrolateral tegumental papillae, testes without deep lobes, and a Laurer's canal pore that opens posterior to the vitelline reservoir and dorsal to the oviducal seminal receptacle. The new species is only the second turtle blood fluke reported from Vietnam.

New Genus of Blood Fluke (Digenea: Schistosomatoidea) from Malaysian Freshwater Turtles (Geoemydidae) and its Phylogenetic Position Within Schistosomatoidea.

: Baracktrema obamai n. gen., n. sp. infects the lung of geoemydid turtles (black marsh turtle, Siebenrockiella crassicollis [type host] and southeast Asian box turtle, Cuora amboinensis ) in the Malaysian states of Perak, Perlis, and Selangor. Baracktrema and Unicaecum Stunkard, 1925 are the only accepted turtle blood fluke genera having the combination of a single cecum, single testis, oviducal seminal receptacle, and uterine pouch. Baracktrema differs from Unicaecum by having a thread-like body approximately 30-50× longer than wide and post-cecal terminal genitalia. Unicaecum has a body approximately 8-12× longer than wide and terminal genitalia that are anterior to the distal end of the cecum. The new genus further differs from all other accepted turtle blood fluke genera by having a cecum that is highly convoluted for its entire length, a spindle-shaped ovary between the cirrus sac and testis, a uterine pouch that loops around the primary vitelline collecting duct, a Laurer's canal, and a dorsal common genital pore. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) revealed, with high nodal support and as predicted by morphology, that Baracktrema and Unicaecum share a recent common ancestor and form a clade sister to the freshwater turtle blood flukes of Spirorchis, paraphyletic Spirhapalum, and Vasotrema and that, collectively, these flukes were sister to all other tetrapod blood flukes (Hapalorhynchus + Griphobilharzia plus the marine turtle blood flukes and schistosomes). Pending a forthcoming emended morphological diagnosis of the family, the clade including Spirorchis spp., paraphyletic Spirhapalum, Vasotrema, Baracktrema, and Unicaecum is a likely placeholder for "Spirorchiidae Stunkard, 1921 " (type genus Spirorchis MacCallum, 1918 ; type species Spirorchis innominatus Ward, 1921 ). The present study comprises the 17th blood fluke known to infect geoemydid turtles and the first proposal of a new genus of turtle blood fluke in 21 yr.

Local host specialization, host-switching, and dispersal shape the regional distributions of avian haemosporidian parasites.

The drivers of regional parasite distributions are poorly understood, especially in comparison with those of free-living species. For vector-transmitted parasites, in particular, distributions might be influenced by host-switching and by parasite dispersal with primary hosts and vectors. We surveyed haemosporidian blood parasites (Plasmodium and Haemoproteus) of small land birds in eastern North America to characterize a regional parasite community. Distributions of parasite populations generally reflected distributions of their hosts across the region. However, when the interdependence between hosts and parasites was controlled statistically, local host assemblages were related to regional climatic gradients, but parasite assemblages were not. Moreover, because parasite assemblage similarity does not decrease with distance when controlling for host assemblages and climate, parasites evidently disperse readily within the distributions of their hosts. The degree of specialization on hosts varied in some parasite lineages over short periods and small geographic distances independently of the diversity of available hosts and potentially competing parasite lineages. Nonrandom spatial turnover was apparent in parasite lineages infecting one host species that was well-sampled within a single year across its range, plausibly reflecting localized adaptations of hosts and parasites. Overall, populations of avian hosts generally determine the geographic distributions of haemosporidian parasites. However, parasites are not dispersal-limited within their host distributions, and they may switch hosts readily.