DOI: 10.5061/dryad.6dn5p
title: Data from: Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia

description: In theory, competition among species in a shared habitat results in niche
 separation. In the case of small recondite mammals such as shrews, little
 is known about their autecologies, leaving open questions regarding the
 degree to which closely related species co-occur and how or whether
 ecological niches are partitioned. The extent to which species are able to
 coexist may depend on the degree to which they exploit different features
 of their habitat, which may in turn influence our ability to recognize
 them as species. We explored these issues in a biodiversity hotspot, by
 surveying shrew (genus Crocidura) diversity on the Indonesian island of
 Java. We sequenced portions of nine unlinked genes in 100–117 specimens of
 Javan shrews and incorporated homologous data from most known Crocidura
 species from other parts of island South-East Asia. Current taxonomy
 recognizes four Crocidura species on Java, including two endemics.
 However, our phylogenetic, population genetic and species delimitation
 analyses identify five species on the island, and all are endemic to Java.
 While the individual ranges of these species may not overlap in their
 entirety, we found up to four species living syntopically and all five
 species co-occurring on one mountain. Differences in species' body
 size, use of above ground-level habitats by one species and habitat
 partitioning along ecological gradients may have facilitated species
 diversification and coexistence.
description: mtDNA
 AlignmentNexus file containing 66
 unique haplotypes of cytochrome b from Southeast Asian shrews. This
 alignment was used to generate the gene tree in Figure
 2.mtDNA.unique.haplotypes.nexApoB AlignmentNexus file containing phased alleles from Apolipoprotein B sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.ApoB.all.java.with.localities.nexBDNF AlignmentNexus file containing phased alleles from BDNF sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.BDNF.all.java.with.localities.nexBRCA1 AlignmentNexus file containing phased alleles from BRCA1 sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.BRCA1.all.java.with.localities.nexGHR AlignmentNexus file containing phased alleles from GHR sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.GHR10.all.java.with.localities.nexMCGF AlignmentNexus file containing phased alleles from MCGF sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.MCGF.all.java.with.localities.nexPTGER4 AlignmentNexus file containing phased alleles from PTGER4 sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.PTGER.all.java.with.localities.nexRAG1 AlignmentNexus file containing phased alleles from RAG1 sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.Rag1.all.java.with.localities.nexvWF AlignmentNexus file containing phased alleles from vWF sequences of Javan Crocidura. This alignment was used to generate the gene tree in Figure S1.vWF.all.java.with.localities.nex