Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus)

We provide a response to a recently published evaluation of the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus). The work we discuss used exon capture genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies, with recommendation that it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of this study, and explain in clearer terms how to interpret genomic analyses for applied management. We identify four broad conceptual issues that led to errant recommendations: (1) interpretation of subspecies and diagnosability, (2) inappropriate use of reciprocal monophyly as a criterion for subspecies, (3) importance of geographic isolation, and (4) error in hypothesis testing and misinterpretation of results. We conclude that the data from this genomic appraisal add to information from prior studies providing strong support for recognition of N. m. atristriatus as a subspecies. Our conclusions have important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.

The probability of joint monophyly of all species in an arbitrary species tree.

Monophyly is a feature of a set of genetic lineages in which every lineage in the set is more closely related to all other members of the set than it is to any lineage outside the set. Multiple sets of lineages that are separately monophyletic are said to be reciprocally monophyletic, or jointly monophyletic. The prevalence of reciprocal monophyly, or joint monophyly, has been used to evaluate phylogenetic and phylogeographic hypotheses, as well as to delimit species. These applications often make use of a probability of joint monophyly under models of gene lineage evolution. Studies in coalescent theory have computed this joint monophyly probability for small numbers of separate groups in arbitrary species trees, and for arbitrary numbers of separate groups in trivial species trees. Here, generalizing existing results on monophyly probabilities under the multispecies coalescent, we derive the probability of joint monophyly for arbitrary numbers of separate groups in arbitrary species trees. We illustrate how our result collapses to previously examined cases. We also study the effect of tree height, sample size, and number of species on the probability of joint monophyly. The result also enables computation of relatively simple lower and upper bounds on the joint monophyly probability. Our results expand the scope of joint monophyly calculations beyond small numbers of species, subsuming past formulas that have been used in simpler cases.

Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777)

The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

Background Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka. Results The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins. Conclusions Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

Misinterpretation of genomic data matters for endangered species listing: the subspecific status of the Peñasco least chipmunk (Neotamias minimus atristriatus)

Puckett et al. (2021. Ecology and Evolution, 11, 12114-12128) evaluated the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus) using genomic approaches and concluded that their results did not support the taxonomic distinction of this endemic mammal as a subspecies and recommended it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of Puckett et al. (2021), and explain in clearer terms how to interpret genomic analyses for applied management. We identify six conceptual issues that led to the faulty interpretations and recommendations: 1) error in hypothesis testing, 2) overlooking statistical support (or lack thereof) of lineages, 3) inappropriate use of reciprocal monophyly as a criterion for subspecies, 4) importance of geographic isolation and inferences from historical biogeography, 5) diagnosable criteria, and 6) importance of phenotype. We conclude that the data of Puckett et al. (2021) add to information from prior studies providing strong support for N. m. atristriatus as a well-defined taxonomic unit at the rank of subspecies (or species). This finding has important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.

Systematics and conservation of an endemic radiation of Accipiter hawks in the Caribbean islands

More than one-third of the bird species found in the Caribbean are endemic to a set of neighboring islands or a single island. However, we have little knowledge of the evolutionary history of the Caribbean avifauna, and the lack of phylogenetic studies limits our understanding of the extent of endemism in the region. The Sharp-shinned Hawk (Accipiter striatus) occurs widely across the Americas and includes 3 endemic Caribbean taxa: venator on Puerto Rico, striatus on Hispaniola, and fringilloides on Cuba. These island populations have undergone extreme declines presumably due to ecosystem changes caused by anthropogenic factors, as well as due to severe hurricanes. Sharp-shinned Hawks, in general, and Caribbean Sharp-shinned Hawks, in particular, have not been placed in a modern phylogenetic context. However, the island taxa have historically been presumed to have some ongoing gene flow with mainland populations. Here we sequenced ultraconserved elements (UCEs) and their flanking regions from 38 samples, focusing on Caribbean taxa. Using a combination of UCEs, mitochondrial genome sequences, and single-nucleotide polymorphisms, we investigated the phylogenetic relationships among Caribbean lineages and their relationships to mainland taxa. We found that Caribbean Sharp-shinned Hawks are reciprocally monophyletic in all datasets with regard to mainland populations and among island taxa (with no shared mtDNA haplotypes) and that divergence in the NADH dehydrogenase 2 gene (ND2) between these mainland and island groups averaged 1.83%. Furthermore, sparse non-negative matrix factorization (sNMF) analysis indicated that Hispaniola, Puerto Rico, and mainland samples each form separate populations with limited admixture. We argue that our findings are consistent with the recognition of the 3 resident Caribbean populations as species-level taxa because nuclear and mitochondrial genetic data indicate reciprocal monophyly and have species-level divergences, there is no sharing of mitochondrial haplotypes among or between island taxa and those on the mainland; and they are diagnosable by plumage.

Morphological groupings within Euphlyctis (Anura: Dicroglossidae) and description of a new species from the surroundings of Thattekad Bird Sanctuary, Kerala, India

The skittering frog genus Euphlyctis is known to have a distribution range from Arabian Peninsula to Bangladesh through India and Sri Lanka. Although species descriptions were initiated about two centuries ago in the genus with a small number of species described, taxonomic identities and genetic information for many species are still incomplete / inaccurate. Here, we report the systematic status of this group, discuss a series of taxonomic issues, and describe a new species. Based on morphological characters and colour patterns, and their reciprocal monophyly in the molecular tree, two morphological groups, ‘cyanophlyctis group’ and ‘hexadactylus group’ are established within the genus Euphlyctis. We discuss the genetic identity for E. cyanophlyctis, described 220 years ago from the Indian subcontinent, from the surroundings of its type locality. E. mudigere is proposed as a junior synonym of E. cyanophlyctis as it was described from populations here considered to originate from the general distribution area of the latter taxon, and without substantial genetic divergence from other populations here attributed to E. cyanophlyctis. The potential of resurrection of Euphlyctis seistanica due to distinct genetic population in Iran is discussed; this lineage appears to be genetically rather similar to E. kalasgramensis, and the species distinctness of these two lineages requires further study. The validity of E. kalasgramensis is also discussed in the context of the historically earlier nomina, Rana bengalensis and Rana leschenaultii due to distribution range overlaps. The prospects of establishing either Rana cyanophlictis variety fulvus or Rana cyanophlictis variety flavens from Sri Lanka are also mentioned. Based on a comparative account, we report the discovery of a new species of skittering frog Euphlyctis kerala sp. nov. which has a restricted distribution in the western coastal plains of India, south of the Palghat gap. [http://zoobank.org/urn:lsid:zoobank.org:act:02B1DE04-C40C-4AAD-AC87-EF97673A4BF5]

The family Epimetopidae (Coleoptera: Hydrophiloidea): review of current knowledge, genus-level phylogeny, and taxonomic revision of Eupotemus

Epimetopidae are a small beetle family of the superfamily Hydrophiloidea, comprising 72 described species in three genera: the American Epimetopus Lacordaire, 1854 (56 species), Asian Eumetopus Balfour-Browne, 1949 (eight species) and African Eupotemus Ji & Jäch, 1998 (eight species, of which six are described as new here). In this study we illustrate and compare the adult morphology of all three genera and generate the first DNA sequences for Eumetopus and Eupotemus. The morphological data and sequences of four genes (cox1, 16S, 18S and 28S) are used to reconstruct phylogenetic relationships among genera. Both strongly support the monophyly of Epimetopidae, reveal Eumetopus as the earliest diverging taxon and Epimetopus + Eupotemus as a strongly supported clade with numerous synapomorphies. The reciprocal monophyly of Epimetopus and Eupotemus is strongly supported by DNA data but not in the morphological analysis which reveals Epimetopus paraphyletic. Eumetopus, despite being the earliest branching clade, is characterized by many unique derived structures, e.g. by the presence of the sperm pump in males (unique in Hydrophiloidea). The available data on the biology of Epimetopidae indicate that most species inhabit sandy to muddy margins of streams or rivers. Females of all three genera carry egg cases; Epimetopidae hence are one of three independent lineages of Hydrophiloidea in which this behavior evolved. Larvae are only known for Epimetopus and are characterized by morphological adaptations for feeding by piercing and sucking, a closed tracheal system and abdominal gills; larvae of Eumetopus and Eupotemus remain unknown and further research is needed to confirm whether they show the same adaptations as Epimetopus. The taxonomy of the African genus Eupotemus is re­vised, with six species described as new: E. bilobatus sp. nov. (Nigeria), E. cameroonensis sp. nov. (Cameroon), E. ophioglossus sp. nov. (Gabon, Togo), E. smithi sp. nov. (Côte d’Ivoire), E. taianus sp. nov. (Côte d’Ivoire) and E. uluguru sp. nov. (Tanzania). Eupotemus limicola Delève, 1967 is fixed as the type species of the genus according to ICZN (1999: Art. 70.3). New records of Eumetopus species are provided (E. acutimontis Ji & Jäch, 1998 from Vietnam, E. bullatus (Sharp, 1875) from India: Maharashtra, E. flavidulus (Sharp, 1890) from India: Maharashtra and Andhra Pradesh, E. maindroni (Régimbart, 1903) from India: Maharashtra and Gujarat, and E. weigeli Skale & Jäch, 2003 from India: Uttarakhand). The habitus of all species is illustrated. An updated checklist of the Epimetopus species is provided, and records of two specimens of the E. costatus group from Zambia and Saudi Arabia are considered to result from either accidental introductions or mislabelling.

Another mystery snail in the Adirondacks: DNA barcoding reveals the first record of Sinotaia cf. quadrata (Caenogastropoda: Viviparidae) from North America

ABSTRACTAlien molluscs pose a serious threat to global freshwater diversity and have been implicated in many ecosystem-altering invasion events over the past few decades. Biomonitoring surveys are therefore a key tool for ensuring biosecurity in diversity hotspots and vulnerable habitats. In this study, we use DNA barcoding to provide the first record of the viviparid, Sinotaia cf. quadrata from North America. Reciprocal monophyly and low genetic divergence (uncorrected p-distance: 0.004) with a Bellamya quadrata individual from the type region (China) provides strong support for this identification. The species was recovered as part of a routine biomonitoring survey of the Adirondack region of northern New York. Only three adults were recovered (no populations or juveniles) indicating that the discovery represents a very recent arrival. Considering the proximity of the sampling site from the massive St. Lawrence River, it is likely that S. cf. quadrata was introduced into the St. Lawrence, probably via the aquarium plant trade, and was able to spread into smaller river system in northern New York and possibly other border states. This record represents the fourth alien viviparid, the third of which is of Asian origin, that have made its way to New York waters. Future biomonitoring efforts for the upcoming summer period will involve targeted searches for S. cf. quadrata to determine the extent of its spread in the region.

Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

Inferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression. In this study, we combined high throughput sequence data (ddRADseq), geometric morphometric information, and novel phylogenetic inference methods that explicitly account for gene flow to infer the evolutionary relationships and the timing and mode of diversification in a complex of Ibero-Maghrebian montane grasshoppers of the subgenus Dreuxius (genus Omocestus). Our analyses supported the phenotypic distinctiveness of most sister taxa, two events of historical introgression involving lineages at different stages of the diversification continuum, and the recent Pleistocene origin (< 1 Ma) of the complex. Phylogenetic analyses did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting overseas migration between the two continents during the Pleistocene. Collectively, these results indicate that periods of isolation and secondary contact linked to Pleistocene glacial cycles likely contributed to both allopatric speciation and post divergence gene flow in the complex. This study exemplifies how the integration of multiple lines of evidence can help to reconstruct complex histories of reticulated evolution and highlights the important role of Quaternary climatic oscillations as a diversification engine in the Ibero-Maghrebian biodiversity hotspot.