Population demography maintains biogeographic boundaries

Global biodiversity is organized into biogeographic regions that comprise distinct biotas. The contemporary factors maintaining differences in species composition between biogeographic regions are poorly understood. Given the evidence that populations with sufficient genetic variation can adapt to fill new habitats, it is surprising that we do not see more homogenization of species assemblages among regions. Theory suggests that the expansion of populations across biogeographic transition zones could be limited by environmental gradients that affect population demography in ways that could limit adaptive capacity, but this has not been empirically explored. Using three independently curated data sets describing continental patterns of mammalian demography and population genetics, we show that populations closer to biogeographic transition zones have lower effective population sizes and genetic diversity, and are more genetically differentiated. These patterns are consistent with reduced adaptive capacity near biogeographic transition zones. The consistency of these patterns across mammalian species suggests they are stable, predictable, and generalizable in their contribution to long-term limits on expansion and homogenization of biodiversity across biogeographic transition zones. Understanding the contemporary processes acting on populations that maintain differences in the composition of regional biotas is crucial for our basic understanding of the current and future organization of global biodiversity. The importance of contemporary, population-level processes on the maintenance of global biogeographic regions suggests that biogeographic boundaries are susceptible to environmental perturbation associated with human-caused global change.

Water Quality Analysis in a Subtropical River with an Adapted Biomonitoring Working Party (BMWP) Index

Subtropical rivers in developing countries often lack adequate monitoring, which makes it difficult to comprehensively determine their water quality when faced with different anthropic impacts. There are no proper protocols in the regulations to incorporate indicators and adapt them to different biogeographic regions, limiting the potential success of conservation and restoration of river ecosystems. This study proposes implementing macroinvertebrates as bioindicators of water quality in river ecosystems, and modifying the calibration of the widely used Biomonitoring Working Party (BMWP) index for its adaptation in a subtropical river. The Duero River, Mexico, was used as an example in this study. Data were explored with multivariate statistics, and the water quality and habitat values were averaged to obtain the families’ bioindication values and the index categories. The BMWP adequately described a deterioration gradient from the origin to the river mouth (from fair to extremely polluted), with some intermediate recovery points related to the presence of springs. Its performance was compared with other biological indices and exhibited a positive relationship with all of them. In addition, how BMWP changed over time was analyzed by examining previous samples, and highlighted increased river deterioration over time. A calibrated BMWP will allow for long-term monitoring at a low cost.

The population genetics characteristics of a 90 locus panel of microhaplotypes

Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.

Two new species and a new species group of Mycodrosophila Oldenberg, 1914 (Diptera: Drosophilidae) from the Amazon

There are 130 described species in the genus Mycodrosophila Oldenberg, 1914, distributed across all biogeographic regions. Most of these species show essential mycophagy. Currently, ten species are known from the Neotropical Region, nine of which are found in the Amazon, Atlantic Forest, Cerrado and Pampa biomes of Brazil. In this study, we describe the adult external morphology and structures of male and/or female terminalia for two new species from the Amazon Biome of Brazil. In addition, we propose a new species group, the Mycodrosophila neoprojectans group, encompassing the two new species described here, together with three previously described species from the Neotropics.

Birds specimens of the zoological collection of the Universidad de Nariño, Colombia

We provide a complete dataset of bird specimens of the zoological collection at the Universidad de Nariño, Colombia. For every specimen, we reviewed taxonomic identifications to species level by applying curatorial procedures, including the comparison of skins, the use of taxonomic keys and primary literature, and by confirming georeferenced locality data. We present 1249 specimens from 419 species. Most records come from ecosystems in southwestern Colombia, department of Nariño. All records are in the Darwin Core standard and have been made available through the Colombian biodiversity portal (SiB-Colombia) and the GBIF. In addition, we projected these bird occurrences in a geographic context to analyze the density, representation of ecosystems, biogeographic regions, and administrative units (municipalities). We also examine the representation of relevant species regarding their endemism, migratory, or conservation status. With this information, we want to support research and training initiatives to support ecological planning with biogeographic approaches to understand the temporal changes in bird faunas.

Species That Fly at a Higher Game: Patterns of Deep–Water Emergence Along the Chilean Coast, Including a Global Review of the Phenomenon

Deep-water emergence (DWE) is the phenomenon where marine species normally found at great depths (i.e., below 200 m), can be found locally occurring in significantly shallower depths (i.e., euphotic zone, usually shallower than 50 m). Although this phenomenon has been previously mentioned and deep-water emergent species have been described from the fjord regions of North America, Scandinavia, and New Zealand, local or global hypotheses to explain this phenomenon have rarely been tested. This publication includes the first literature review on DWE. Our knowledge of distribution patterns of Chilean marine invertebrates is still very scarce, especially from habitats below SCUBA diving depth. In our databases, we have been gathering occurrence data of more than 1000 invertebrate species along the Chilean coast, both from our research and from the literature. We also distributed a list of 50 common and easily in situ-identifiable species among biologically experienced sport divers along the Chilean coast and recorded their sighting reports. Among other findings, the analysis of the data revealed patterns from 28 species and six genera with similar longitudinal and bathymetric distribution along the entire Chilean coast: along the Chilean coast these species are typically restricted to deep water (>200 m) but only in some parts of Chilean Patagonia (>39°S–56°S), the same species are also common to locally abundant at diving depths (<30 m). We found 28 of these ‘deep’ species present in shallow-water of North Patagonia, 32 in Central Patagonia and 12 in South Patagonia. The species belong to the phyla Cnidaria (six species), Mollusca (four species), Arthropoda (two species) and Echinodermata (16 species). We ran several analyses comparing depth distribution between biogeographic regions (two-way ANOVA) and comparing abiotic parameters of shallow and deep sites to search for correlations of distribution with environmental variables (Generalized Linear Models). For the analyses, we used a total of 3328 presence points and 10635 absence points. The results of the statistical analysis of the parameters used, however, did not reveal conclusive results. We summarize cases from other fjord regions and discuss hypotheses of DWE from the literature for Chilean Patagonia.

Mitochondrial DNA suggests the existence of two distinct species in Moluccas and New Guinea within Nyctimystes infrafrenatus (Günther, 1867)

Sulaeman TN, Hamidy A, Farajallah A, Fouquet A, Riyanto A, Arida E, Mulyadi, Trilaksono W, Munir M. 2021. Mitochondrial DNA suggests the existence of two distinct species in Moluccas and New Guinea within Nyctimystes infrafrenatus (Günther, 1867). Biodiversitas 22: 3287-3297. Nyctimystes infrafrenatus is a widespread frog species distributed across northern Australia, New Guinea, Bismarck archipelago and in the eastern part of Indonesian archipelago. The species thus encompasses two biogeographic regions, Papua and Wallacea. We evaluated the phylogenetic relationships among the populations from Papua and Moluccas based on two mitochondrial loci (16S rRNA and Cytochrome Oxidase Subunit I). Two major subclades are recovered within Nyctimystes infrafrenatus with subclade A being represented by populations from New Guinea and northern Australia and subclade B by Moluccan populations (Halmahera and Tidore). Genetic distances (2.3-4.2% in 16S rRNA) between these subclades suggest they could belong to distinct species. Since New Guinea populations correspond to the nominal species and that Nyctimystes tennuigranulatus (Boettger 1895), currently considered as a junior synonym of Nyctimystes infrafrenatus, is available for the northern Moluccan populations, we proposed to remove this taxon from synonymy. However, samples used in this study come from northern Moluccas, further studies including samples from Ambon (where another synonym was described i.e. Calamita dolichopsis) is needed to determine the taxonomic status of the southern Moluccan population whether they are conspecific with northern Moluccan population or not.

Global distribution and richness of Armillaria species inferred from public databases and amplicon sequencing datasets

Armillaria is a globally distributed fungal genus most notably recognized as economically important plant pathogens that are found predominantly in forest and agronomic systems. Armillaria has more recently received attention for ecologically diverse roles as woody plant decomposers and as mycorrhizal symbionts with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets. In order to assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer pairs for the ribosomal operon. Our estimates reveal that species richness ranges from 50 to 60 species, depending on which marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.

The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus

Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2,395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.